Updated sample htmlcoverage-4.4

1 files changed, 921 insertions, 917 deletions

diff --git a/doc/sample_html/cogapp_cogapp_py.html b/doc/sample_html/cogapp_cogapp_py.html
index 3d730b9e..378bf12c 100644
--- a/doc/sample_html/cogapp_cogapp_py.html
+++ b/doc/sample_html/cogapp_cogapp_py.html
@@ -8,7 +8,7 @@
     
     
     <meta http-equiv="X-UA-Compatible" content="IE=emulateIE7" />
-    <title>Coverage for cogapp/cogapp.py: 47.10%</title>
+    <title>Coverage for cogapp/cogapp.py: 47.12%</title>
     <link rel="stylesheet" href="style.css" type="text/css">
     
     <script type="text/javascript" src="jquery.min.js"></script>
@@ -24,19 +24,19 @@
 <div id="header">
     <div class="content">
         <h1>Coverage for <b>cogapp/cogapp.py</b> :
-            <span class="pc_cov">47.10%</span>
+            <span class="pc_cov">47.12%</span>
         </h1>
 
         <img id="keyboard_icon" src="keybd_closed.png" alt="Show keyboard shortcuts" />
 
         <h2 class="stats">
-            427 statements &nbsp;
-            <span class="run hide_run shortkey_r button_toggle_run">230 run</span>
-            <span class="mis shortkey_m button_toggle_mis">197 missing</span>
+            429 statements &nbsp;
+            <span class="run hide_run shortkey_r button_toggle_run">231 run</span>
+            <span class="mis shortkey_m button_toggle_mis">198 missing</span>
             <span class="exc shortkey_x button_toggle_exc">4 excluded</span>
 
             
-                <span class="par run hide_run shortkey_p button_toggle_par">26 partial</span>
+                <span class="par run hide_run shortkey_p button_toggle_par">27 partial</span>
             
         </h2>
     </div>
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-<p id="n173" class="pln"><a href="#n173">173</a></p>
+<p id="n172" class="stm par run hide_run"><a href="#n172">172</a></p>
+<p id="n173" class="stm mis"><a href="#n173">173</a></p>
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+<p id="n176" class="stm run hide_run"><a href="#n176">176</a></p>
+<p id="n177" class="pln"><a href="#n177">177</a></p>
+<p id="n178" class="pln"><a href="#n178">178</a></p>
+<p id="n179" class="stm run hide_run"><a href="#n179">179</a></p>
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+<p id="n203" class="pln"><a href="#n203">203</a></p>
+<p id="n204" class="stm run hide_run"><a href="#n204">204</a></p>
+<p id="n205" class="stm run hide_run"><a href="#n205">205</a></p>
+<p id="n206" class="pln"><a href="#n206">206</a></p>
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+<p id="n208" class="stm run hide_run"><a href="#n208">208</a></p>
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+<p id="n238" class="stm run hide_run"><a href="#n238">238</a></p>
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+<p id="n258" class="pln"><a href="#n258">258</a></p>
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 <p id="n380" class="stm mis"><a href="#n380">380</a></p>
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 <p id="n383" class="pln"><a href="#n383">383</a></p>
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 <p id="n385" class="pln"><a href="#n385">385</a></p>
 <p id="n386" class="pln"><a href="#n386">386</a></p>
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+<p id="n388" class="pln"><a href="#n388">388</a></p>
 <p id="n389" class="stm run hide_run"><a href="#n389">389</a></p>
-<p id="n390" class="pln"><a href="#n390">390</a></p>
-<p id="n391" class="stm par run hide_run"><a href="#n391">391</a></p>
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 <p id="n392" class="pln"><a href="#n392">392</a></p>
-<p id="n393" class="stm mis"><a href="#n393">393</a></p>
-<p id="n394" class="stm mis"><a href="#n394">394</a></p>
-<p id="n395" class="stm par run hide_run"><a href="#n395">395</a></p>
-<p id="n396" class="pln"><a href="#n396">396</a></p>
-<p id="n397" class="stm mis"><a href="#n397">397</a></p>
-<p id="n398" class="stm mis"><a href="#n398">398</a></p>
-<p id="n399" class="pln"><a href="#n399">399</a></p>
-<p id="n400" class="stm run hide_run"><a href="#n400">400</a></p>
-<p id="n401" class="stm run hide_run"><a href="#n401">401</a></p>
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+<p id="n396" class="stm mis"><a href="#n396">396</a></p>
+<p id="n397" class="stm par run hide_run"><a href="#n397">397</a></p>
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+<p id="n399" class="stm mis"><a href="#n399">399</a></p>
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 <p id="n403" class="stm run hide_run"><a href="#n403">403</a></p>
 <p id="n404" class="pln"><a href="#n404">404</a></p>
 <p id="n405" class="stm run hide_run"><a href="#n405">405</a></p>
-<p id="n406" class="stm run hide_run"><a href="#n406">406</a></p>
-<p id="n407" class="pln"><a href="#n407">407</a></p>
-<p id="n408" class="pln"><a href="#n408">408</a></p>
-<p id="n409" class="stm par run hide_run"><a href="#n409">409</a></p>
-<p id="n410" class="stm run hide_run"><a href="#n410">410</a></p>
-<p id="n411" class="pln"><a href="#n411">411</a></p>
-<p id="n412" class="pln"><a href="#n412">412</a></p>
-<p id="n413" class="stm run hide_run"><a href="#n413">413</a></p>
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+<p id="n407" class="stm run hide_run"><a href="#n407">407</a></p>
+<p id="n408" class="stm run hide_run"><a href="#n408">408</a></p>
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+<p id="n411" class="stm par run hide_run"><a href="#n411">411</a></p>
+<p id="n412" class="stm run hide_run"><a href="#n412">412</a></p>
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 <p id="n414" class="pln"><a href="#n414">414</a></p>
-<p id="n415" class="pln"><a href="#n415">415</a></p>
-<p id="n416" class="stm run hide_run"><a href="#n416">416</a></p>
-<p id="n417" class="stm run hide_run"><a href="#n417">417</a></p>
-<p id="n418" class="pln"><a href="#n418">418</a></p>
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+<p id="n417" class="pln"><a href="#n417">417</a></p>
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 <p id="n419" class="stm run hide_run"><a href="#n419">419</a></p>
-<p id="n420" class="stm par run hide_run"><a href="#n420">420</a></p>
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-<p id="n423" class="stm par run hide_run"><a href="#n423">423</a></p>
-<p id="n424" class="stm mis"><a href="#n424">424</a></p>
-<p id="n425" class="pln"><a href="#n425">425</a></p>
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-<p id="n427" class="stm run hide_run"><a href="#n427">427</a></p>
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 <p id="n428" class="stm run hide_run"><a href="#n428">428</a></p>
 <p id="n429" class="stm run hide_run"><a href="#n429">429</a></p>
-<p id="n430" class="stm par run hide_run"><a href="#n430">430</a></p>
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 <p id="n431" class="stm run hide_run"><a href="#n431">431</a></p>
-<p id="n432" class="pln"><a href="#n432">432</a></p>
-<p id="n433" class="pln"><a href="#n433">433</a></p>
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-<p id="n435" class="stm run hide_run"><a href="#n435">435</a></p>
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+<p id="n435" class="pln"><a href="#n435">435</a></p>
 <p id="n436" class="stm run hide_run"><a href="#n436">436</a></p>
 <p id="n437" class="stm run hide_run"><a href="#n437">437</a></p>
 <p id="n438" class="stm run hide_run"><a href="#n438">438</a></p>
-<p id="n439" class="pln"><a href="#n439">439</a></p>
-<p id="n440" class="pln"><a href="#n440">440</a></p>
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 <p id="n441" class="pln"><a href="#n441">441</a></p>
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-<p id="n443" class="stm run hide_run"><a href="#n443">443</a></p>
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 <p id="n444" class="stm run hide_run"><a href="#n444">444</a></p>
 <p id="n445" class="stm run hide_run"><a href="#n445">445</a></p>
 <p id="n446" class="stm run hide_run"><a href="#n446">446</a></p>
-<p id="n447" class="pln"><a href="#n447">447</a></p>
-<p id="n448" class="pln"><a href="#n448">448</a></p>
-<p id="n449" class="stm run hide_run"><a href="#n449">449</a></p>
-<p id="n450" class="stm run hide_run"><a href="#n450">450</a></p>
-<p id="n451" class="pln"><a href="#n451">451</a></p>
-<p id="n452" class="pln"><a href="#n452">452</a></p>
-<p id="n453" class="stm run hide_run"><a href="#n453">453</a></p>
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 <p id="n454" class="pln"><a href="#n454">454</a></p>
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-<p id="n457" class="stm par run hide_run"><a href="#n457">457</a></p>
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-<p id="n460" class="stm par run hide_run"><a href="#n460">460</a></p>
-<p id="n461" class="stm mis"><a href="#n461">461</a></p>
-<p id="n462" class="pln"><a href="#n462">462</a></p>
-<p id="n463" class="stm par run hide_run"><a href="#n463">463</a></p>
-<p id="n464" class="stm run hide_run"><a href="#n464">464</a></p>
-<p id="n465" class="stm run hide_run"><a href="#n465">465</a></p>
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 <p id="n466" class="stm run hide_run"><a href="#n466">466</a></p>
-<p id="n467" class="stm par run hide_run"><a href="#n467">467</a></p>
-<p id="n468" class="stm mis"><a href="#n468">468</a></p>
-<p id="n469" class="pln"><a href="#n469">469</a></p>
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 <p id="n471" class="pln"><a href="#n471">471</a></p>
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-<p id="n473" class="stm run hide_run"><a href="#n473">473</a></p>
-<p id="n474" class="stm run hide_run"><a href="#n474">474</a></p>
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 <p id="n476" class="stm run hide_run"><a href="#n476">476</a></p>
 <p id="n477" class="pln"><a href="#n477">477</a></p>
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 <p id="n479" class="pln"><a href="#n479">479</a></p>
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 <p id="n482" class="stm run hide_run"><a href="#n482">482</a></p>
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-<p id="n490" class="stm run hide_run"><a href="#n490">490</a></p>
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 <p id="n491" class="stm run hide_run"><a href="#n491">491</a></p>
 <p id="n492" class="stm run hide_run"><a href="#n492">492</a></p>
-<p id="n493" class="pln"><a href="#n493">493</a></p>
-<p id="n494" class="stm par run hide_run"><a href="#n494">494</a></p>
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 <p id="n495" class="pln"><a href="#n495">495</a></p>
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 <p id="n497" class="pln"><a href="#n497">497</a></p>
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 <p id="n499" class="pln"><a href="#n499">499</a></p>
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 <p id="n501" class="pln"><a href="#n501">501</a></p>
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 <p id="n503" class="pln"><a href="#n503">503</a></p>
-<p id="n504" class="stm run hide_run"><a href="#n504">504</a></p>
-<p id="n505" class="stm par run hide_run"><a href="#n505">505</a></p>
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 <p id="n506" class="stm run hide_run"><a href="#n506">506</a></p>
-<p id="n507" class="stm run hide_run"><a href="#n507">507</a></p>
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 <p id="n508" class="stm run hide_run"><a href="#n508">508</a></p>
 <p id="n509" class="stm run hide_run"><a href="#n509">509</a></p>
 <p id="n510" class="stm run hide_run"><a href="#n510">510</a></p>
 <p id="n511" class="stm run hide_run"><a href="#n511">511</a></p>
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 <p id="n513" class="stm run hide_run"><a href="#n513">513</a></p>
 <p id="n514" class="pln"><a href="#n514">514</a></p>
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-<p id="n517" class="stm par run hide_run"><a href="#n517">517</a></p>
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 <p id="n520" class="stm mis"><a href="#n520">520</a></p>
 <p id="n521" class="stm mis"><a href="#n521">521</a></p>
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-<p id="n523" class="pln"><a href="#n523">523</a></p>
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 <p id="n525" class="pln"><a href="#n525">525</a></p>
-<p id="n526" class="pln"><a href="#n526">526</a></p>
-<p id="n527" class="stm mis"><a href="#n527">527</a></p>
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-<p id="n529" class="pln"><a href="#n529">529</a></p>
-<p id="n530" class="pln"><a href="#n530">530</a></p>
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 <p id="n531" class="pln"><a href="#n531">531</a></p>
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-<p id="n536" class="stm run hide_run"><a href="#n536">536</a></p>
-<p id="n537" class="stm run hide_run"><a href="#n537">537</a></p>
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+<p id="n538" class="stm run hide_run"><a href="#n538">538</a></p>
+<p id="n539" class="stm run hide_run"><a href="#n539">539</a></p>
+<p id="n540" class="pln"><a href="#n540">540</a></p>
+<p id="n541" class="stm par run hide_run"><a href="#n541">541</a></p>
+<p id="n542" class="stm mis"><a href="#n542">542</a></p>
+<p id="n543" class="pln"><a href="#n543">543</a></p>
 <p id="n544" class="stm par run hide_run"><a href="#n544">544</a></p>
 <p id="n545" class="stm mis"><a href="#n545">545</a></p>
-<p id="n546" class="pln"><a href="#n546">546</a></p>
-<p id="n547" class="pln"><a href="#n547">547</a></p>
+<p id="n546" class="stm par run hide_run"><a href="#n546">546</a></p>
+<p id="n547" class="stm mis"><a href="#n547">547</a></p>
 <p id="n548" class="pln"><a href="#n548">548</a></p>
-<p id="n549" class="stm run hide_run"><a href="#n549">549</a></p>
+<p id="n549" class="pln"><a href="#n549">549</a></p>
 <p id="n550" class="pln"><a href="#n550">550</a></p>
 <p id="n551" class="stm run hide_run"><a href="#n551">551</a></p>
 <p id="n552" class="pln"><a href="#n552">552</a></p>
-<p id="n553" class="pln"><a href="#n553">553</a></p>
+<p id="n553" class="stm run hide_run"><a href="#n553">553</a></p>
 <p id="n554" class="pln"><a href="#n554">554</a></p>
-<p id="n555" class="stm par run hide_run"><a href="#n555">555</a></p>
+<p id="n555" class="pln"><a href="#n555">555</a></p>
 <p id="n556" class="pln"><a href="#n556">556</a></p>
-<p id="n557" class="stm mis"><a href="#n557">557</a></p>
-<p id="n558" class="stm mis"><a href="#n558">558</a></p>
-<p id="n559" class="stm run hide_run"><a href="#n559">559</a></p>
-<p id="n560" class="pln"><a href="#n560">560</a></p>
+<p id="n557" class="stm par run hide_run"><a href="#n557">557</a></p>
+<p id="n558" class="pln"><a href="#n558">558</a></p>
+<p id="n559" class="stm mis"><a href="#n559">559</a></p>
+<p id="n560" class="stm mis"><a href="#n560">560</a></p>
 <p id="n561" class="stm run hide_run"><a href="#n561">561</a></p>
 <p id="n562" class="pln"><a href="#n562">562</a></p>
-<p id="n563" class="pln"><a href="#n563">563</a></p>
+<p id="n563" class="stm run hide_run"><a href="#n563">563</a></p>
 <p id="n564" class="pln"><a href="#n564">564</a></p>
-<p id="n565" class="stm run hide_run"><a href="#n565">565</a></p>
-<p id="n566" class="stm run hide_run"><a href="#n566">566</a></p>
+<p id="n565" class="pln"><a href="#n565">565</a></p>
+<p id="n566" class="pln"><a href="#n566">566</a></p>
 <p id="n567" class="stm run hide_run"><a href="#n567">567</a></p>
 <p id="n568" class="stm run hide_run"><a href="#n568">568</a></p>
-<p id="n569" class="pln"><a href="#n569">569</a></p>
+<p id="n569" class="stm run hide_run"><a href="#n569">569</a></p>
 <p id="n570" class="stm run hide_run"><a href="#n570">570</a></p>
 <p id="n571" class="pln"><a href="#n571">571</a></p>
-<p id="n572" class="pln"><a href="#n572">572</a></p>
-<p id="n573" class="stm mis"><a href="#n573">573</a></p>
+<p id="n572" class="stm run hide_run"><a href="#n572">572</a></p>
+<p id="n573" class="pln"><a href="#n573">573</a></p>
 <p id="n574" class="pln"><a href="#n574">574</a></p>
 <p id="n575" class="stm mis"><a href="#n575">575</a></p>
 <p id="n576" class="pln"><a href="#n576">576</a></p>
 <p id="n577" class="stm mis"><a href="#n577">577</a></p>
-<p id="n578" class="stm mis"><a href="#n578">578</a></p>
+<p id="n578" class="pln"><a href="#n578">578</a></p>
 <p id="n579" class="stm mis"><a href="#n579">579</a></p>
 <p id="n580" class="stm mis"><a href="#n580">580</a></p>
-<p id="n581" class="pln"><a href="#n581">581</a></p>
-<p id="n582" class="pln"><a href="#n582">582</a></p>
-<p id="n583" class="stm mis"><a href="#n583">583</a></p>
-<p id="n584" class="stm mis"><a href="#n584">584</a></p>
+<p id="n581" class="stm mis"><a href="#n581">581</a></p>
+<p id="n582" class="stm mis"><a href="#n582">582</a></p>
+<p id="n583" class="pln"><a href="#n583">583</a></p>
+<p id="n584" class="pln"><a href="#n584">584</a></p>
 <p id="n585" class="stm mis"><a href="#n585">585</a></p>
 <p id="n586" class="stm mis"><a href="#n586">586</a></p>
-<p id="n587" class="pln"><a href="#n587">587</a></p>
-<p id="n588" class="stm run hide_run"><a href="#n588">588</a></p>
-<p id="n589" class="stm mis"><a href="#n589">589</a></p>
-<p id="n590" class="stm mis"><a href="#n590">590</a></p>
-<p id="n591" class="pln"><a href="#n591">591</a></p>
-<p id="n592" class="stm run hide_run"><a href="#n592">592</a></p>
-<p id="n593" class="stm mis"><a href="#n593">593</a></p>
-<p id="n594" class="stm mis"><a href="#n594">594</a></p>
+<p id="n587" class="stm mis"><a href="#n587">587</a></p>
+<p id="n588" class="stm mis"><a href="#n588">588</a></p>
+<p id="n589" class="pln"><a href="#n589">589</a></p>
+<p id="n590" class="stm run hide_run"><a href="#n590">590</a></p>
+<p id="n591" class="stm mis"><a href="#n591">591</a></p>
+<p id="n592" class="stm mis"><a href="#n592">592</a></p>
+<p id="n593" class="pln"><a href="#n593">593</a></p>
+<p id="n594" class="stm run hide_run"><a href="#n594">594</a></p>
 <p id="n595" class="stm mis"><a href="#n595">595</a></p>
-<p id="n596" class="pln"><a href="#n596">596</a></p>
-<p id="n597" class="stm run hide_run"><a href="#n597">597</a></p>
-<p id="n598" class="stm mis"><a href="#n598">598</a></p>
-<p id="n599" class="stm mis"><a href="#n599">599</a></p>
-<p id="n600" class="pln"><a href="#n600">600</a></p>
-<p id="n601" class="stm run hide_run"><a href="#n601">601</a></p>
+<p id="n596" class="stm mis"><a href="#n596">596</a></p>
+<p id="n597" class="stm mis"><a href="#n597">597</a></p>
+<p id="n598" class="pln"><a href="#n598">598</a></p>
+<p id="n599" class="stm run hide_run"><a href="#n599">599</a></p>
+<p id="n600" class="stm mis"><a href="#n600">600</a></p>
+<p id="n601" class="stm mis"><a href="#n601">601</a></p>
 <p id="n602" class="pln"><a href="#n602">602</a></p>
-<p id="n603" class="pln"><a href="#n603">603</a></p>
+<p id="n603" class="stm run hide_run"><a href="#n603">603</a></p>
 <p id="n604" class="pln"><a href="#n604">604</a></p>
-<p id="n605" class="stm mis"><a href="#n605">605</a></p>
-<p id="n606" class="stm mis"><a href="#n606">606</a></p>
-<p id="n607" class="pln"><a href="#n607">607</a></p>
+<p id="n605" class="pln"><a href="#n605">605</a></p>
+<p id="n606" class="pln"><a href="#n606">606</a></p>
+<p id="n607" class="stm mis"><a href="#n607">607</a></p>
 <p id="n608" class="stm mis"><a href="#n608">608</a></p>
-<p id="n609" class="stm mis"><a href="#n609">609</a></p>
-<p id="n610" class="pln"><a href="#n610">610</a></p>
-<p id="n611" class="pln"><a href="#n611">611</a></p>
-<p id="n612" class="stm mis"><a href="#n612">612</a></p>
+<p id="n609" class="pln"><a href="#n609">609</a></p>
+<p id="n610" class="stm mis"><a href="#n610">610</a></p>
+<p id="n611" class="stm mis"><a href="#n611">611</a></p>
+<p id="n612" class="pln"><a href="#n612">612</a></p>
 <p id="n613" class="pln"><a href="#n613">613</a></p>
-<p id="n614" class="pln"><a href="#n614">614</a></p>
-<p id="n615" class="stm mis"><a href="#n615">615</a></p>
-<p id="n616" class="stm mis"><a href="#n616">616</a></p>
+<p id="n614" class="stm mis"><a href="#n614">614</a></p>
+<p id="n615" class="pln"><a href="#n615">615</a></p>
+<p id="n616" class="pln"><a href="#n616">616</a></p>
 <p id="n617" class="stm mis"><a href="#n617">617</a></p>
-<p id="n618" class="pln"><a href="#n618">618</a></p>
-<p id="n619" class="pln"><a href="#n619">619</a></p>
-<p id="n620" class="stm mis"><a href="#n620">620</a></p>
-<p id="n621" class="stm mis"><a href="#n621">621</a></p>
+<p id="n618" class="stm mis"><a href="#n618">618</a></p>
+<p id="n619" class="stm mis"><a href="#n619">619</a></p>
+<p id="n620" class="pln"><a href="#n620">620</a></p>
+<p id="n621" class="pln"><a href="#n621">621</a></p>
 <p id="n622" class="stm mis"><a href="#n622">622</a></p>
-<p id="n623" class="pln"><a href="#n623">623</a></p>
+<p id="n623" class="stm mis"><a href="#n623">623</a></p>
 <p id="n624" class="stm mis"><a href="#n624">624</a></p>
-<p id="n625" class="stm mis"><a href="#n625">625</a></p>
+<p id="n625" class="pln"><a href="#n625">625</a></p>
 <p id="n626" class="stm mis"><a href="#n626">626</a></p>
 <p id="n627" class="stm mis"><a href="#n627">627</a></p>
 <p id="n628" class="stm mis"><a href="#n628">628</a></p>
@@ -704,85 +704,85 @@
 <p id="n633" class="stm mis"><a href="#n633">633</a></p>
 <p id="n634" class="stm mis"><a href="#n634">634</a></p>
 <p id="n635" class="stm mis"><a href="#n635">635</a></p>
-<p id="n636" class="pln"><a href="#n636">636</a></p>
-<p id="n637" class="pln"><a href="#n637">637</a></p>
+<p id="n636" class="stm mis"><a href="#n636">636</a></p>
+<p id="n637" class="stm mis"><a href="#n637">637</a></p>
 <p id="n638" class="pln"><a href="#n638">638</a></p>
 <p id="n639" class="pln"><a href="#n639">639</a></p>
 <p id="n640" class="pln"><a href="#n640">640</a></p>
-<p id="n641" class="stm mis"><a href="#n641">641</a></p>
-<p id="n642" class="stm mis"><a href="#n642">642</a></p>
-<p id="n643" class="pln"><a href="#n643">643</a></p>
+<p id="n641" class="pln"><a href="#n641">641</a></p>
+<p id="n642" class="pln"><a href="#n642">642</a></p>
+<p id="n643" class="stm mis"><a href="#n643">643</a></p>
 <p id="n644" class="stm mis"><a href="#n644">644</a></p>
 <p id="n645" class="pln"><a href="#n645">645</a></p>
 <p id="n646" class="stm mis"><a href="#n646">646</a></p>
 <p id="n647" class="pln"><a href="#n647">647</a></p>
-<p id="n648" class="stm run hide_run"><a href="#n648">648</a></p>
+<p id="n648" class="stm mis"><a href="#n648">648</a></p>
 <p id="n649" class="pln"><a href="#n649">649</a></p>
-<p id="n650" class="pln"><a href="#n650">650</a></p>
-<p id="n651" class="stm mis"><a href="#n651">651</a></p>
-<p id="n652" class="stm mis"><a href="#n652">652</a></p>
+<p id="n650" class="stm run hide_run"><a href="#n650">650</a></p>
+<p id="n651" class="pln"><a href="#n651">651</a></p>
+<p id="n652" class="pln"><a href="#n652">652</a></p>
 <p id="n653" class="stm mis"><a href="#n653">653</a></p>
 <p id="n654" class="stm mis"><a href="#n654">654</a></p>
-<p id="n655" class="pln"><a href="#n655">655</a></p>
+<p id="n655" class="stm mis"><a href="#n655">655</a></p>
 <p id="n656" class="stm mis"><a href="#n656">656</a></p>
-<p id="n657" class="stm mis"><a href="#n657">657</a></p>
+<p id="n657" class="pln"><a href="#n657">657</a></p>
 <p id="n658" class="stm mis"><a href="#n658">658</a></p>
-<p id="n659" class="pln"><a href="#n659">659</a></p>
+<p id="n659" class="stm mis"><a href="#n659">659</a></p>
 <p id="n660" class="stm mis"><a href="#n660">660</a></p>
-<p id="n661" class="stm mis"><a href="#n661">661</a></p>
+<p id="n661" class="pln"><a href="#n661">661</a></p>
 <p id="n662" class="stm mis"><a href="#n662">662</a></p>
 <p id="n663" class="stm mis"><a href="#n663">663</a></p>
-<p id="n664" class="pln"><a href="#n664">664</a></p>
-<p id="n665" class="stm run hide_run"><a href="#n665">665</a></p>
+<p id="n664" class="stm mis"><a href="#n664">664</a></p>
+<p id="n665" class="stm mis"><a href="#n665">665</a></p>
 <p id="n666" class="pln"><a href="#n666">666</a></p>
-<p id="n667" class="pln"><a href="#n667">667</a></p>
-<p id="n668" class="stm mis"><a href="#n668">668</a></p>
-<p id="n669" class="stm mis"><a href="#n669">669</a></p>
-<p id="n670" class="pln"><a href="#n670">670</a></p>
+<p id="n667" class="stm run hide_run"><a href="#n667">667</a></p>
+<p id="n668" class="pln"><a href="#n668">668</a></p>
+<p id="n669" class="pln"><a href="#n669">669</a></p>
+<p id="n670" class="stm mis"><a href="#n670">670</a></p>
 <p id="n671" class="stm mis"><a href="#n671">671</a></p>
-<p id="n672" class="stm mis"><a href="#n672">672</a></p>
-<p id="n673" class="pln"><a href="#n673">673</a></p>
+<p id="n672" class="pln"><a href="#n672">672</a></p>
+<p id="n673" class="stm mis"><a href="#n673">673</a></p>
 <p id="n674" class="stm mis"><a href="#n674">674</a></p>
-<p id="n675" class="stm mis"><a href="#n675">675</a></p>
+<p id="n675" class="pln"><a href="#n675">675</a></p>
 <p id="n676" class="stm mis"><a href="#n676">676</a></p>
 <p id="n677" class="stm mis"><a href="#n677">677</a></p>
-<p id="n678" class="pln"><a href="#n678">678</a></p>
+<p id="n678" class="stm mis"><a href="#n678">678</a></p>
 <p id="n679" class="stm mis"><a href="#n679">679</a></p>
 <p id="n680" class="pln"><a href="#n680">680</a></p>
 <p id="n681" class="stm mis"><a href="#n681">681</a></p>
 <p id="n682" class="pln"><a href="#n682">682</a></p>
-<p id="n683" class="stm run hide_run"><a href="#n683">683</a></p>
+<p id="n683" class="stm mis"><a href="#n683">683</a></p>
 <p id="n684" class="pln"><a href="#n684">684</a></p>
-<p id="n685" class="pln"><a href="#n685">685</a></p>
+<p id="n685" class="stm run hide_run"><a href="#n685">685</a></p>
 <p id="n686" class="pln"><a href="#n686">686</a></p>
 <p id="n687" class="pln"><a href="#n687">687</a></p>
-<p id="n688" class="stm mis"><a href="#n688">688</a></p>
+<p id="n688" class="pln"><a href="#n688">688</a></p>
 <p id="n689" class="pln"><a href="#n689">689</a></p>
-<p id="n690" class="pln"><a href="#n690">690</a></p>
-<p id="n691" class="stm mis"><a href="#n691">691</a></p>
-<p id="n692" class="stm mis"><a href="#n692">692</a></p>
+<p id="n690" class="stm mis"><a href="#n690">690</a></p>
+<p id="n691" class="pln"><a href="#n691">691</a></p>
+<p id="n692" class="pln"><a href="#n692">692</a></p>
 <p id="n693" class="stm mis"><a href="#n693">693</a></p>
-<p id="n694" class="pln"><a href="#n694">694</a></p>
+<p id="n694" class="stm mis"><a href="#n694">694</a></p>
 <p id="n695" class="stm mis"><a href="#n695">695</a></p>
-<p id="n696" class="stm mis"><a href="#n696">696</a></p>
+<p id="n696" class="pln"><a href="#n696">696</a></p>
 <p id="n697" class="stm mis"><a href="#n697">697</a></p>
-<p id="n698" class="pln"><a href="#n698">698</a></p>
+<p id="n698" class="stm mis"><a href="#n698">698</a></p>
 <p id="n699" class="stm mis"><a href="#n699">699</a></p>
-<p id="n700" class="stm mis"><a href="#n700">700</a></p>
+<p id="n700" class="pln"><a href="#n700">700</a></p>
 <p id="n701" class="stm mis"><a href="#n701">701</a></p>
-<p id="n702" class="pln"><a href="#n702">702</a></p>
+<p id="n702" class="stm mis"><a href="#n702">702</a></p>
 <p id="n703" class="stm mis"><a href="#n703">703</a></p>
-<p id="n704" class="stm mis"><a href="#n704">704</a></p>
+<p id="n704" class="pln"><a href="#n704">704</a></p>
 <p id="n705" class="stm mis"><a href="#n705">705</a></p>
-<p id="n706" class="pln"><a href="#n706">706</a></p>
+<p id="n706" class="stm mis"><a href="#n706">706</a></p>
 <p id="n707" class="stm mis"><a href="#n707">707</a></p>
 <p id="n708" class="pln"><a href="#n708">708</a></p>
-<p id="n709" class="stm run hide_run"><a href="#n709">709</a></p>
+<p id="n709" class="stm mis"><a href="#n709">709</a></p>
 <p id="n710" class="pln"><a href="#n710">710</a></p>
-<p id="n711" class="pln"><a href="#n711">711</a></p>
+<p id="n711" class="stm run hide_run"><a href="#n711">711</a></p>
 <p id="n712" class="pln"><a href="#n712">712</a></p>
-<p id="n713" class="stm mis"><a href="#n713">713</a></p>
-<p id="n714" class="stm mis"><a href="#n714">714</a></p>
+<p id="n713" class="pln"><a href="#n713">713</a></p>
+<p id="n714" class="pln"><a href="#n714">714</a></p>
 <p id="n715" class="stm mis"><a href="#n715">715</a></p>
 <p id="n716" class="stm mis"><a href="#n716">716</a></p>
 <p id="n717" class="stm mis"><a href="#n717">717</a></p>
@@ -797,8 +797,8 @@
 <p id="n726" class="stm mis"><a href="#n726">726</a></p>
 <p id="n727" class="stm mis"><a href="#n727">727</a></p>
 <p id="n728" class="stm mis"><a href="#n728">728</a></p>
-<p id="n729" class="pln"><a href="#n729">729</a></p>
-<p id="n730" class="pln"><a href="#n730">730</a></p>
+<p id="n729" class="stm mis"><a href="#n729">729</a></p>
+<p id="n730" class="stm mis"><a href="#n730">730</a></p>
 <p id="n731" class="pln"><a href="#n731">731</a></p>
 <p id="n732" class="pln"><a href="#n732">732</a></p>
 <p id="n733" class="pln"><a href="#n733">733</a></p>
@@ -850,6 +850,8 @@
 <p id="n779" class="pln"><a href="#n779">779</a></p>
 <p id="n780" class="pln"><a href="#n780">780</a></p>
 <p id="n781" class="pln"><a href="#n781">781</a></p>
+<p id="n782" class="pln"><a href="#n782">782</a></p>
+<p id="n783" class="pln"><a href="#n783">783</a></p>
 
             </td>
             <td class="text">
@@ -1024,616 +1026,618 @@
 <p id="t169" class="stm run hide_run">            <span class="nam">sOut</span> <span class="op">=</span> <span class="str">'\n'</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">lines</span><span class="op">)</span><span class="op">+</span><span class="str">'\n'</span><span class="strut">&nbsp;</span></p>
 <p id="t170" class="stm run hide_run">        <span class="key">if</span> <span class="nam">dedent</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
 <p id="t171" class="stm run hide_run">            <span class="nam">sOut</span> <span class="op">=</span> <span class="nam">reindentBlock</span><span class="op">(</span><span class="nam">sOut</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t172" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">outstring</span> <span class="op">+=</span> <span class="nam">sOut</span><span class="strut">&nbsp;</span></p>
-<p id="t173" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t174" class="stm run hide_run">    <span class="key">def</span> <span class="nam">outl</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">sOut</span><span class="op">=</span><span class="str">''</span><span class="op">,</span> <span class="op">**</span><span class="nam">kw</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t175" class="pln">        <span class="str">""" The cog.outl function.</span><span class="strut">&nbsp;</span></p>
-<p id="t176" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
-<p id="t177" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">out</span><span class="op">(</span><span class="nam">sOut</span><span class="op">,</span> <span class="op">**</span><span class="nam">kw</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t178" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">out</span><span class="op">(</span><span class="str">'\n'</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t179" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t180" class="stm run hide_run">    <span class="key">def</span> <span class="nam">error</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">msg</span><span class="op">=</span><span class="str">'Error raised by cog generator.'</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t181" class="pln">        <span class="str">""" The cog.error function.</span><span class="strut">&nbsp;</span></p>
-<p id="t182" class="pln"><span class="str">            Instead of raising standard python errors, cog generators can use</span><span class="strut">&nbsp;</span></p>
-<p id="t183" class="pln"><span class="str">            this function.  It will display the error without a scary Python</span><span class="strut">&nbsp;</span></p>
-<p id="t184" class="pln"><span class="str">            traceback.</span><span class="strut">&nbsp;</span></p>
-<p id="t185" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
-<p id="t186" class="stm mis">        <span class="key">raise</span> <span class="nam">CogGeneratedError</span><span class="op">(</span><span class="nam">msg</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t187" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t188" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t189" class="stm run hide_run"><span class="key">class</span> <span class="nam">NumberedFileReader</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t190" class="pln">    <span class="str">""" A decorator for files that counts the readline()'s called.</span><span class="strut">&nbsp;</span></p>
-<p id="t191" class="pln"><span class="str">    """</span><span class="strut">&nbsp;</span></p>
-<p id="t192" class="stm run hide_run">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">f</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t193" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">f</span> <span class="op">=</span> <span class="nam">f</span><span class="strut">&nbsp;</span></p>
-<p id="t194" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">n</span> <span class="op">=</span> <span class="num">0</span><span class="strut">&nbsp;</span></p>
-<p id="t195" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t196" class="stm run hide_run">    <span class="key">def</span> <span class="nam">readline</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t197" class="stm run hide_run">        <span class="nam">l</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">f</span><span class="op">.</span><span class="nam">readline</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t198" class="stm run hide_run">        <span class="key">if</span> <span class="nam">l</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t199" class="stm run hide_run">            <span class="nam">self</span><span class="op">.</span><span class="nam">n</span> <span class="op">+=</span> <span class="num">1</span><span class="strut">&nbsp;</span></p>
-<p id="t200" class="stm run hide_run">        <span class="key">return</span> <span class="nam">l</span><span class="strut">&nbsp;</span></p>
-<p id="t201" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t202" class="stm run hide_run">    <span class="key">def</span> <span class="nam">linenumber</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t203" class="stm run hide_run">        <span class="key">return</span> <span class="nam">self</span><span class="op">.</span><span class="nam">n</span><span class="strut">&nbsp;</span></p>
-<p id="t204" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t205" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t206" class="stm run hide_run"><span class="key">class</span> <span class="nam">CogOptions</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t207" class="pln">    <span class="str">""" Options for a run of cog.</span><span class="strut">&nbsp;</span></p>
-<p id="t208" class="pln"><span class="str">    """</span><span class="strut">&nbsp;</span></p>
-<p id="t209" class="stm run hide_run">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t210" class="pln">        <span class="com"># Defaults for argument values.</span><span class="strut">&nbsp;</span></p>
-<p id="t211" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">args</span> <span class="op">=</span> <span class="op">[</span><span class="op">]</span><span class="strut">&nbsp;</span></p>
-<p id="t212" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">includePath</span> <span class="op">=</span> <span class="op">[</span><span class="op">]</span><span class="strut">&nbsp;</span></p>
-<p id="t213" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">defines</span> <span class="op">=</span> <span class="op">{</span><span class="op">}</span><span class="strut">&nbsp;</span></p>
-<p id="t214" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">bShowVersion</span> <span class="op">=</span> <span class="nam">False</span><span class="strut">&nbsp;</span></p>
-<p id="t215" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">sMakeWritableCmd</span> <span class="op">=</span> <span class="nam">None</span><span class="strut">&nbsp;</span></p>
-<p id="t216" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">bReplace</span> <span class="op">=</span> <span class="nam">False</span><span class="strut">&nbsp;</span></p>
-<p id="t217" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">bNoGenerate</span> <span class="op">=</span> <span class="nam">False</span><span class="strut">&nbsp;</span></p>
-<p id="t218" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">sOutputName</span> <span class="op">=</span> <span class="nam">None</span><span class="strut">&nbsp;</span></p>
-<p id="t219" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">bWarnEmpty</span> <span class="op">=</span> <span class="nam">False</span><span class="strut">&nbsp;</span></p>
-<p id="t220" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">bHashOutput</span> <span class="op">=</span> <span class="nam">False</span><span class="strut">&nbsp;</span></p>
-<p id="t221" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">bDeleteCode</span> <span class="op">=</span> <span class="nam">False</span><span class="strut">&nbsp;</span></p>
-<p id="t222" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">bEofCanBeEnd</span> <span class="op">=</span> <span class="nam">False</span><span class="strut">&nbsp;</span></p>
-<p id="t223" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">sSuffix</span> <span class="op">=</span> <span class="nam">None</span><span class="strut">&nbsp;</span></p>
-<p id="t224" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">bNewlines</span> <span class="op">=</span> <span class="nam">False</span><span class="strut">&nbsp;</span></p>
-<p id="t225" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">sBeginSpec</span> <span class="op">=</span> <span class="str">'[[[cog'</span><span class="strut">&nbsp;</span></p>
-<p id="t226" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">sEndSpec</span> <span class="op">=</span> <span class="str">']]]'</span><span class="strut">&nbsp;</span></p>
-<p id="t227" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">sEndOutput</span> <span class="op">=</span> <span class="str">'[[[end]]]'</span><span class="strut">&nbsp;</span></p>
-<p id="t228" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">sEncoding</span> <span class="op">=</span> <span class="str">"utf-8"</span><span class="strut">&nbsp;</span></p>
-<p id="t229" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">verbosity</span> <span class="op">=</span> <span class="num">2</span><span class="strut">&nbsp;</span></p>
-<p id="t230" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t231" class="stm run hide_run">    <span class="key">def</span> <span class="nam">__eq__</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">other</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t232" class="pln">        <span class="str">""" Comparison operator for tests to use.</span><span class="strut">&nbsp;</span></p>
-<p id="t233" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
-<p id="t234" class="stm mis">        <span class="key">return</span> <span class="nam">self</span><span class="op">.</span><span class="nam">__dict__</span> <span class="op">==</span> <span class="nam">other</span><span class="op">.</span><span class="nam">__dict__</span><span class="strut">&nbsp;</span></p>
-<p id="t235" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t236" class="stm run hide_run">    <span class="key">def</span> <span class="nam">clone</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t237" class="pln">        <span class="str">""" Make a clone of these options, for further refinement.</span><span class="strut">&nbsp;</span></p>
-<p id="t238" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
-<p id="t239" class="stm mis">        <span class="key">return</span> <span class="nam">copy</span><span class="op">.</span><span class="nam">deepcopy</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t240" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t241" class="stm run hide_run">    <span class="key">def</span> <span class="nam">addToIncludePath</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">dirs</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t242" class="pln">        <span class="str">""" Add directories to the include path.</span><span class="strut">&nbsp;</span></p>
-<p id="t243" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
-<p id="t244" class="stm mis">        <span class="nam">dirs</span> <span class="op">=</span> <span class="nam">dirs</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="nam">os</span><span class="op">.</span><span class="nam">pathsep</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t245" class="stm mis">        <span class="nam">self</span><span class="op">.</span><span class="nam">includePath</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="nam">dirs</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t246" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t247" class="stm run hide_run">    <span class="key">def</span> <span class="nam">parseArgs</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">argv</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t248" class="pln">        <span class="com"># Parse the command line arguments.</span><span class="strut">&nbsp;</span></p>
-<p id="t249" class="stm mis">        <span class="key">try</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t250" class="stm mis">            <span class="nam">opts</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">args</span> <span class="op">=</span> <span class="nam">getopt</span><span class="op">.</span><span class="nam">getopt</span><span class="op">(</span><span class="strut">&nbsp;</span></p>
-<p id="t251" class="pln">                <span class="nam">argv</span><span class="op">,</span><span class="strut">&nbsp;</span></p>
-<p id="t252" class="pln">                <span class="str">'cdD:eI:n:o:rs:Uvw:xz'</span><span class="op">,</span><span class="strut">&nbsp;</span></p>
-<p id="t253" class="pln">                <span class="op">[</span><span class="strut">&nbsp;</span></p>
-<p id="t254" class="pln">                    <span class="str">'markers='</span><span class="op">,</span><span class="strut">&nbsp;</span></p>
-<p id="t255" class="pln">                    <span class="str">'verbosity='</span><span class="op">,</span><span class="strut">&nbsp;</span></p>
-<p id="t256" class="pln">                <span class="op">]</span><span class="strut">&nbsp;</span></p>
-<p id="t257" class="pln">            <span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t258" class="stm mis">        <span class="key">except</span> <span class="nam">getopt</span><span class="op">.</span><span class="nam">error</span> <span class="key">as</span> <span class="nam">msg</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t259" class="stm mis">            <span class="key">raise</span> <span class="nam">CogUsageError</span><span class="op">(</span><span class="nam">msg</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t260" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t261" class="pln">        <span class="com"># Handle the command line arguments.</span><span class="strut">&nbsp;</span></p>
-<p id="t262" class="stm mis">        <span class="key">for</span> <span class="nam">o</span><span class="op">,</span> <span class="nam">a</span> <span class="key">in</span> <span class="nam">opts</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t263" class="stm mis">            <span class="key">if</span> <span class="nam">o</span> <span class="op">==</span> <span class="str">'-c'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t264" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">bHashOutput</span> <span class="op">=</span> <span class="nam">True</span><span class="strut">&nbsp;</span></p>
-<p id="t265" class="stm mis">            <span class="key">elif</span> <span class="nam">o</span> <span class="op">==</span> <span class="str">'-d'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t266" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">bDeleteCode</span> <span class="op">=</span> <span class="nam">True</span><span class="strut">&nbsp;</span></p>
-<p id="t267" class="stm mis">            <span class="key">elif</span> <span class="nam">o</span> <span class="op">==</span> <span class="str">'-D'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t268" class="stm mis">                <span class="key">if</span> <span class="nam">a</span><span class="op">.</span><span class="nam">count</span><span class="op">(</span><span class="str">'='</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">1</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t269" class="stm mis">                    <span class="key">raise</span> <span class="nam">CogUsageError</span><span class="op">(</span><span class="str">"-D takes a name=value argument"</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t270" class="stm mis">                <span class="nam">name</span><span class="op">,</span> <span class="nam">value</span> <span class="op">=</span> <span class="nam">a</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="str">'='</span><span class="op">,</span> <span class="num">1</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t271" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">defines</span><span class="op">[</span><span class="nam">name</span><span class="op">]</span> <span class="op">=</span> <span class="nam">value</span><span class="strut">&nbsp;</span></p>
-<p id="t272" class="stm mis">            <span class="key">elif</span> <span class="nam">o</span> <span class="op">==</span> <span class="str">'-e'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t273" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">bWarnEmpty</span> <span class="op">=</span> <span class="nam">True</span><span class="strut">&nbsp;</span></p>
-<p id="t274" class="stm mis">            <span class="key">elif</span> <span class="nam">o</span> <span class="op">==</span> <span class="str">'-I'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t275" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">addToIncludePath</span><span class="op">(</span><span class="nam">a</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t276" class="stm mis">            <span class="key">elif</span> <span class="nam">o</span> <span class="op">==</span> <span class="str">'-n'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t277" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">sEncoding</span> <span class="op">=</span> <span class="nam">a</span><span class="strut">&nbsp;</span></p>
-<p id="t278" class="stm mis">            <span class="key">elif</span> <span class="nam">o</span> <span class="op">==</span> <span class="str">'-o'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t279" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">sOutputName</span> <span class="op">=</span> <span class="nam">a</span><span class="strut">&nbsp;</span></p>
-<p id="t280" class="stm mis">            <span class="key">elif</span> <span class="nam">o</span> <span class="op">==</span> <span class="str">'-r'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t281" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">bReplace</span> <span class="op">=</span> <span class="nam">True</span><span class="strut">&nbsp;</span></p>
-<p id="t282" class="stm mis">            <span class="key">elif</span> <span class="nam">o</span> <span class="op">==</span> <span class="str">'-s'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t283" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">sSuffix</span> <span class="op">=</span> <span class="nam">a</span><span class="strut">&nbsp;</span></p>
-<p id="t284" class="stm mis">            <span class="key">elif</span> <span class="nam">o</span> <span class="op">==</span> <span class="str">'-U'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t285" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">bNewlines</span> <span class="op">=</span> <span class="nam">True</span><span class="strut">&nbsp;</span></p>
-<p id="t286" class="stm mis">            <span class="key">elif</span> <span class="nam">o</span> <span class="op">==</span> <span class="str">'-v'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t287" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">bShowVersion</span> <span class="op">=</span> <span class="nam">True</span><span class="strut">&nbsp;</span></p>
-<p id="t288" class="stm mis">            <span class="key">elif</span> <span class="nam">o</span> <span class="op">==</span> <span class="str">'-w'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t289" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">sMakeWritableCmd</span> <span class="op">=</span> <span class="nam">a</span><span class="strut">&nbsp;</span></p>
-<p id="t290" class="stm mis">            <span class="key">elif</span> <span class="nam">o</span> <span class="op">==</span> <span class="str">'-x'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t291" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">bNoGenerate</span> <span class="op">=</span> <span class="nam">True</span><span class="strut">&nbsp;</span></p>
-<p id="t292" class="stm mis">            <span class="key">elif</span> <span class="nam">o</span> <span class="op">==</span> <span class="str">'-z'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t293" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">bEofCanBeEnd</span> <span class="op">=</span> <span class="nam">True</span><span class="strut">&nbsp;</span></p>
-<p id="t294" class="stm mis">            <span class="key">elif</span> <span class="nam">o</span> <span class="op">==</span> <span class="str">'--markers'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t295" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">_parse_markers</span><span class="op">(</span><span class="nam">a</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t296" class="stm mis">            <span class="key">elif</span> <span class="nam">o</span> <span class="op">==</span> <span class="str">'--verbosity'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t297" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">verbosity</span> <span class="op">=</span> <span class="nam">int</span><span class="op">(</span><span class="nam">a</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t298" class="pln">            <span class="key">else</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t299" class="pln">                <span class="com"># Since getopt.getopt is given a list of possible flags,</span><span class="strut">&nbsp;</span></p>
-<p id="t300" class="pln">                <span class="com"># this is an internal error.</span><span class="strut">&nbsp;</span></p>
-<p id="t301" class="exc">                <span class="key">raise</span> <span class="nam">CogInternalError</span><span class="op">(</span><span class="str">"Don't understand argument %s"</span> <span class="op">%</span> <span class="nam">o</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t302" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t303" class="stm run hide_run">    <span class="key">def</span> <span class="nam">_parse_markers</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">val</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t304" class="stm mis">        <span class="key">try</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t305" class="stm mis">            <span class="nam">self</span><span class="op">.</span><span class="nam">sBeginSpec</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sEndSpec</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sEndOutput</span> <span class="op">=</span> <span class="nam">val</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="str">' '</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t306" class="stm mis">        <span class="key">except</span> <span class="nam">ValueError</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t307" class="stm mis">            <span class="key">raise</span> <span class="nam">CogUsageError</span><span class="op">(</span><span class="strut">&nbsp;</span></p>
-<p id="t308" class="pln">                <span class="str">'--markers requires 3 values separated by spaces, could not parse %r'</span> <span class="op">%</span> <span class="nam">val</span><span class="strut">&nbsp;</span></p>
-<p id="t309" class="pln">            <span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t310" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t311" class="stm run hide_run">    <span class="key">def</span> <span class="nam">validate</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t312" class="pln">        <span class="str">""" Does nothing if everything is OK, raises CogError's if it's not.</span><span class="strut">&nbsp;</span></p>
-<p id="t313" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
-<p id="t314" class="stm mis">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">bReplace</span> <span class="key">and</span> <span class="nam">self</span><span class="op">.</span><span class="nam">bDeleteCode</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t315" class="stm mis">            <span class="key">raise</span> <span class="nam">CogUsageError</span><span class="op">(</span><span class="str">"Can't use -d with -r (or you would delete all your source!)"</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t316" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t317" class="stm mis">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">bReplace</span> <span class="key">and</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sOutputName</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t318" class="stm mis">            <span class="key">raise</span> <span class="nam">CogUsageError</span><span class="op">(</span><span class="str">"Can't use -o with -r (they are opposites)"</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t319" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t320" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t321" class="stm run hide_run"><span class="key">class</span> <span class="nam">Cog</span><span class="op">(</span><span class="nam">Redirectable</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t322" class="pln">    <span class="str">""" The Cog engine.</span><span class="strut">&nbsp;</span></p>
-<p id="t323" class="pln"><span class="str">    """</span><span class="strut">&nbsp;</span></p>
-<p id="t324" class="stm run hide_run">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t325" class="stm run hide_run">        <span class="nam">Redirectable</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t326" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">options</span> <span class="op">=</span> <span class="nam">CogOptions</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t327" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">_fixEndOutputPatterns</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t328" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">installCogModule</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t329" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t330" class="stm run hide_run">    <span class="key">def</span> <span class="nam">_fixEndOutputPatterns</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t331" class="stm run hide_run">        <span class="nam">end_output</span> <span class="op">=</span> <span class="nam">re</span><span class="op">.</span><span class="nam">escape</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sEndOutput</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t332" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">reEndOutput</span> <span class="op">=</span> <span class="nam">re</span><span class="op">.</span><span class="nam">compile</span><span class="op">(</span><span class="nam">end_output</span> <span class="op">+</span> <span class="str">r'(?P&lt;hashsect> *\(checksum: (?P&lt;hash>[a-f0-9]+)\))'</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t333" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">sEndFormat</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sEndOutput</span> <span class="op">+</span> <span class="str">' (checksum: %s)'</span><span class="strut">&nbsp;</span></p>
-<p id="t334" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t335" class="stm run hide_run">    <span class="key">def</span> <span class="nam">showWarning</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">msg</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t336" class="stm mis">        <span class="nam">self</span><span class="op">.</span><span class="nam">prout</span><span class="op">(</span><span class="str">"Warning: "</span><span class="op">+</span><span class="nam">msg</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t337" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t338" class="stm run hide_run">    <span class="key">def</span> <span class="nam">isBeginSpecLine</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">s</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t339" class="stm run hide_run">        <span class="key">return</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sBeginSpec</span> <span class="key">in</span> <span class="nam">s</span><span class="strut">&nbsp;</span></p>
-<p id="t340" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t341" class="stm run hide_run">    <span class="key">def</span> <span class="nam">isEndSpecLine</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">s</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t342" class="stm run hide_run">        <span class="key">return</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sEndSpec</span> <span class="key">in</span> <span class="nam">s</span> <span class="key">and</span> <span class="key">not</span> <span class="nam">self</span><span class="op">.</span><span class="nam">isEndOutputLine</span><span class="op">(</span><span class="nam">s</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t343" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t344" class="stm run hide_run">    <span class="key">def</span> <span class="nam">isEndOutputLine</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">s</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t345" class="stm run hide_run">        <span class="key">return</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sEndOutput</span> <span class="key">in</span> <span class="nam">s</span><span class="strut">&nbsp;</span></p>
-<p id="t346" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t347" class="stm run hide_run">    <span class="key">def</span> <span class="nam">installCogModule</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t348" class="pln">        <span class="str">""" Magic mumbo-jumbo so that imported Python modules</span><span class="strut">&nbsp;</span></p>
-<p id="t349" class="pln"><span class="str">            can say "import cog" and get our state.</span><span class="strut">&nbsp;</span></p>
-<p id="t350" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
-<p id="t351" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">cogmodule</span> <span class="op">=</span> <span class="nam">imp</span><span class="op">.</span><span class="nam">new_module</span><span class="op">(</span><span class="str">'cog'</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t352" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">cogmodule</span><span class="op">.</span><span class="nam">path</span> <span class="op">=</span> <span class="op">[</span><span class="op">]</span><span class="strut">&nbsp;</span></p>
-<p id="t353" class="stm run hide_run">        <span class="nam">sys</span><span class="op">.</span><span class="nam">modules</span><span class="op">[</span><span class="str">'cog'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">cogmodule</span><span class="strut">&nbsp;</span></p>
-<p id="t354" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t355" class="stm run hide_run">    <span class="key">def</span> <span class="nam">openOutputFile</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">fname</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t356" class="pln">        <span class="str">""" Open an output file, taking all the details into account.</span><span class="strut">&nbsp;</span></p>
-<p id="t357" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
-<p id="t358" class="stm mis">        <span class="nam">opts</span> <span class="op">=</span> <span class="op">{</span><span class="op">}</span><span class="strut">&nbsp;</span></p>
-<p id="t359" class="stm mis">        <span class="nam">mode</span> <span class="op">=</span> <span class="str">"w"</span><span class="strut">&nbsp;</span></p>
-<p id="t360" class="stm mis">        <span class="key">if</span> <span class="nam">PY3</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t361" class="stm mis">            <span class="nam">opts</span><span class="op">[</span><span class="str">'encoding'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sEncoding</span><span class="strut">&nbsp;</span></p>
-<p id="t362" class="stm mis">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">bNewlines</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t363" class="stm mis">            <span class="key">if</span> <span class="nam">PY3</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t364" class="stm mis">                <span class="nam">opts</span><span class="op">[</span><span class="str">'newline'</span><span class="op">]</span> <span class="op">=</span> <span class="str">"\n"</span><span class="strut">&nbsp;</span></p>
-<p id="t365" class="pln">            <span class="key">else</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t366" class="stm mis">                <span class="nam">mode</span> <span class="op">=</span> <span class="str">"wb"</span><span class="strut">&nbsp;</span></p>
-<p id="t367" class="stm mis">        <span class="nam">fdir</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">dirname</span><span class="op">(</span><span class="nam">fname</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t368" class="stm mis">        <span class="key">if</span> <span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">dirname</span><span class="op">(</span><span class="nam">fdir</span><span class="op">)</span> <span class="key">and</span> <span class="key">not</span> <span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">exists</span><span class="op">(</span><span class="nam">fdir</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t369" class="stm mis">            <span class="nam">os</span><span class="op">.</span><span class="nam">makedirs</span><span class="op">(</span><span class="nam">fdir</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t370" class="stm mis">        <span class="key">return</span> <span class="nam">open</span><span class="op">(</span><span class="nam">fname</span><span class="op">,</span> <span class="nam">mode</span><span class="op">,</span> <span class="op">**</span><span class="nam">opts</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t371" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t372" class="stm run hide_run">    <span class="key">def</span> <span class="nam">openInputFile</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">fname</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t373" class="pln">        <span class="str">""" Open an input file. """</span><span class="strut">&nbsp;</span></p>
-<p id="t374" class="stm mis">        <span class="key">if</span> <span class="nam">fname</span> <span class="op">==</span> <span class="str">"-"</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t375" class="stm mis">            <span class="key">return</span> <span class="nam">sys</span><span class="op">.</span><span class="nam">stdin</span><span class="strut">&nbsp;</span></p>
-<p id="t376" class="pln">        <span class="key">else</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t377" class="stm mis">            <span class="nam">opts</span> <span class="op">=</span> <span class="op">{</span><span class="op">}</span><span class="strut">&nbsp;</span></p>
-<p id="t378" class="stm mis">            <span class="key">if</span> <span class="nam">PY3</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t379" class="stm mis">                <span class="nam">opts</span><span class="op">[</span><span class="str">'encoding'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sEncoding</span><span class="strut">&nbsp;</span></p>
-<p id="t380" class="stm mis">            <span class="key">return</span> <span class="nam">open</span><span class="op">(</span><span class="nam">fname</span><span class="op">,</span> <span class="str">"r"</span><span class="op">,</span> <span class="op">**</span><span class="nam">opts</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t381" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t382" class="stm run hide_run">    <span class="key">def</span> <span class="nam">processFile</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">fIn</span><span class="op">,</span> <span class="nam">fOut</span><span class="op">,</span> <span class="nam">fname</span><span class="op">=</span><span class="nam">None</span><span class="op">,</span> <span class="nam">globals</span><span class="op">=</span><span class="nam">None</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t383" class="pln">        <span class="str">""" Process an input file object to an output file object.</span><span class="strut">&nbsp;</span></p>
-<p id="t384" class="pln"><span class="str">            fIn and fOut can be file objects, or file names.</span><span class="strut">&nbsp;</span></p>
-<p id="t385" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
-<p id="t386" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t387" class="stm run hide_run">        <span class="nam">sFileIn</span> <span class="op">=</span> <span class="nam">fname</span> <span class="key">or</span> <span class="str">''</span><span class="strut">&nbsp;</span></p>
-<p id="t388" class="stm run hide_run">        <span class="nam">sFileOut</span> <span class="op">=</span> <span class="nam">fname</span> <span class="key">or</span> <span class="str">''</span><span class="strut">&nbsp;</span></p>
-<p id="t389" class="stm run hide_run">        <span class="nam">fInToClose</span> <span class="op">=</span> <span class="nam">fOutToClose</span> <span class="op">=</span> <span class="nam">None</span><span class="strut">&nbsp;</span></p>
-<p id="t390" class="pln">        <span class="com"># Convert filenames to files.</span><span class="strut">&nbsp;</span></p>
-<p id="t391" class="stm par run hide_run"><span class="annotate short">391&#x202F;&#x219B;&#x202F;393</span><span class="annotate long">line 391 didn't jump to line 393, because the condition on line 391 was never true</span>        <span class="key">if</span> <span class="nam">isinstance</span><span class="op">(</span><span class="nam">fIn</span><span class="op">,</span> <span class="nam">string_types</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t392" class="pln">            <span class="com"># Open the input file.</span><span class="strut">&nbsp;</span></p>
-<p id="t393" class="stm mis">            <span class="nam">sFileIn</span> <span class="op">=</span> <span class="nam">fIn</span><span class="strut">&nbsp;</span></p>
-<p id="t394" class="stm mis">            <span class="nam">fIn</span> <span class="op">=</span> <span class="nam">fInToClose</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">openInputFile</span><span class="op">(</span><span class="nam">fIn</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t395" class="stm par run hide_run"><span class="annotate short">395&#x202F;&#x219B;&#x202F;397</span><span class="annotate long">line 395 didn't jump to line 397, because the condition on line 395 was never true</span>        <span class="key">if</span> <span class="nam">isinstance</span><span class="op">(</span><span class="nam">fOut</span><span class="op">,</span> <span class="nam">string_types</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t396" class="pln">            <span class="com"># Open the output file.</span><span class="strut">&nbsp;</span></p>
-<p id="t397" class="stm mis">            <span class="nam">sFileOut</span> <span class="op">=</span> <span class="nam">fOut</span><span class="strut">&nbsp;</span></p>
-<p id="t398" class="stm mis">            <span class="nam">fOut</span> <span class="op">=</span> <span class="nam">fOutToClose</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">openOutputFile</span><span class="op">(</span><span class="nam">fOut</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t399" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t400" class="stm run hide_run">        <span class="key">try</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t401" class="stm run hide_run">            <span class="nam">fIn</span> <span class="op">=</span> <span class="nam">NumberedFileReader</span><span class="op">(</span><span class="nam">fIn</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t402" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t403" class="stm run hide_run">            <span class="nam">bSawCog</span> <span class="op">=</span> <span class="nam">False</span><span class="strut">&nbsp;</span></p>
+<p id="t172" class="stm par run hide_run"><span class="annotate short">172&#x202F;&#x219B;&#x202F;173</span><span class="annotate long">line 172 didn't jump to line 173, because the condition on line 172 was never true</span>        <span class="key">if</span> <span class="key">not</span> <span class="nam">PY3</span> <span class="key">and</span> <span class="nam">isinstance</span><span class="op">(</span><span class="nam">sOut</span><span class="op">,</span> <span class="nam">unicode</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t173" class="stm mis">            <span class="nam">sOut</span> <span class="op">=</span> <span class="nam">sOut</span><span class="op">.</span><span class="nam">encode</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sEncoding</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t174" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">outstring</span> <span class="op">+=</span> <span class="nam">sOut</span><span class="strut">&nbsp;</span></p>
+<p id="t175" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t176" class="stm run hide_run">    <span class="key">def</span> <span class="nam">outl</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">sOut</span><span class="op">=</span><span class="str">''</span><span class="op">,</span> <span class="op">**</span><span class="nam">kw</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t177" class="pln">        <span class="str">""" The cog.outl function.</span><span class="strut">&nbsp;</span></p>
+<p id="t178" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
+<p id="t179" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">out</span><span class="op">(</span><span class="nam">sOut</span><span class="op">,</span> <span class="op">**</span><span class="nam">kw</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t180" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">out</span><span class="op">(</span><span class="str">'\n'</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t181" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t182" class="stm run hide_run">    <span class="key">def</span> <span class="nam">error</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">msg</span><span class="op">=</span><span class="str">'Error raised by cog generator.'</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t183" class="pln">        <span class="str">""" The cog.error function.</span><span class="strut">&nbsp;</span></p>
+<p id="t184" class="pln"><span class="str">            Instead of raising standard python errors, cog generators can use</span><span class="strut">&nbsp;</span></p>
+<p id="t185" class="pln"><span class="str">            this function.  It will display the error without a scary Python</span><span class="strut">&nbsp;</span></p>
+<p id="t186" class="pln"><span class="str">            traceback.</span><span class="strut">&nbsp;</span></p>
+<p id="t187" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
+<p id="t188" class="stm mis">        <span class="key">raise</span> <span class="nam">CogGeneratedError</span><span class="op">(</span><span class="nam">msg</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t189" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t190" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t191" class="stm run hide_run"><span class="key">class</span> <span class="nam">NumberedFileReader</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t192" class="pln">    <span class="str">""" A decorator for files that counts the readline()'s called.</span><span class="strut">&nbsp;</span></p>
+<p id="t193" class="pln"><span class="str">    """</span><span class="strut">&nbsp;</span></p>
+<p id="t194" class="stm run hide_run">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">f</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t195" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">f</span> <span class="op">=</span> <span class="nam">f</span><span class="strut">&nbsp;</span></p>
+<p id="t196" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">n</span> <span class="op">=</span> <span class="num">0</span><span class="strut">&nbsp;</span></p>
+<p id="t197" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t198" class="stm run hide_run">    <span class="key">def</span> <span class="nam">readline</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t199" class="stm run hide_run">        <span class="nam">l</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">f</span><span class="op">.</span><span class="nam">readline</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t200" class="stm run hide_run">        <span class="key">if</span> <span class="nam">l</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t201" class="stm run hide_run">            <span class="nam">self</span><span class="op">.</span><span class="nam">n</span> <span class="op">+=</span> <span class="num">1</span><span class="strut">&nbsp;</span></p>
+<p id="t202" class="stm run hide_run">        <span class="key">return</span> <span class="nam">l</span><span class="strut">&nbsp;</span></p>
+<p id="t203" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t204" class="stm run hide_run">    <span class="key">def</span> <span class="nam">linenumber</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t205" class="stm run hide_run">        <span class="key">return</span> <span class="nam">self</span><span class="op">.</span><span class="nam">n</span><span class="strut">&nbsp;</span></p>
+<p id="t206" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t207" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t208" class="stm run hide_run"><span class="key">class</span> <span class="nam">CogOptions</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t209" class="pln">    <span class="str">""" Options for a run of cog.</span><span class="strut">&nbsp;</span></p>
+<p id="t210" class="pln"><span class="str">    """</span><span class="strut">&nbsp;</span></p>
+<p id="t211" class="stm run hide_run">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t212" class="pln">        <span class="com"># Defaults for argument values.</span><span class="strut">&nbsp;</span></p>
+<p id="t213" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">args</span> <span class="op">=</span> <span class="op">[</span><span class="op">]</span><span class="strut">&nbsp;</span></p>
+<p id="t214" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">includePath</span> <span class="op">=</span> <span class="op">[</span><span class="op">]</span><span class="strut">&nbsp;</span></p>
+<p id="t215" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">defines</span> <span class="op">=</span> <span class="op">{</span><span class="op">}</span><span class="strut">&nbsp;</span></p>
+<p id="t216" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">bShowVersion</span> <span class="op">=</span> <span class="nam">False</span><span class="strut">&nbsp;</span></p>
+<p id="t217" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">sMakeWritableCmd</span> <span class="op">=</span> <span class="nam">None</span><span class="strut">&nbsp;</span></p>
+<p id="t218" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">bReplace</span> <span class="op">=</span> <span class="nam">False</span><span class="strut">&nbsp;</span></p>
+<p id="t219" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">bNoGenerate</span> <span class="op">=</span> <span class="nam">False</span><span class="strut">&nbsp;</span></p>
+<p id="t220" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">sOutputName</span> <span class="op">=</span> <span class="nam">None</span><span class="strut">&nbsp;</span></p>
+<p id="t221" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">bWarnEmpty</span> <span class="op">=</span> <span class="nam">False</span><span class="strut">&nbsp;</span></p>
+<p id="t222" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">bHashOutput</span> <span class="op">=</span> <span class="nam">False</span><span class="strut">&nbsp;</span></p>
+<p id="t223" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">bDeleteCode</span> <span class="op">=</span> <span class="nam">False</span><span class="strut">&nbsp;</span></p>
+<p id="t224" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">bEofCanBeEnd</span> <span class="op">=</span> <span class="nam">False</span><span class="strut">&nbsp;</span></p>
+<p id="t225" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">sSuffix</span> <span class="op">=</span> <span class="nam">None</span><span class="strut">&nbsp;</span></p>
+<p id="t226" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">bNewlines</span> <span class="op">=</span> <span class="nam">False</span><span class="strut">&nbsp;</span></p>
+<p id="t227" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">sBeginSpec</span> <span class="op">=</span> <span class="str">'[[[cog'</span><span class="strut">&nbsp;</span></p>
+<p id="t228" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">sEndSpec</span> <span class="op">=</span> <span class="str">']]]'</span><span class="strut">&nbsp;</span></p>
+<p id="t229" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">sEndOutput</span> <span class="op">=</span> <span class="str">'[[[end]]]'</span><span class="strut">&nbsp;</span></p>
+<p id="t230" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">sEncoding</span> <span class="op">=</span> <span class="str">"utf-8"</span><span class="strut">&nbsp;</span></p>
+<p id="t231" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">verbosity</span> <span class="op">=</span> <span class="num">2</span><span class="strut">&nbsp;</span></p>
+<p id="t232" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t233" class="stm run hide_run">    <span class="key">def</span> <span class="nam">__eq__</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">other</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t234" class="pln">        <span class="str">""" Comparison operator for tests to use.</span><span class="strut">&nbsp;</span></p>
+<p id="t235" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
+<p id="t236" class="stm mis">        <span class="key">return</span> <span class="nam">self</span><span class="op">.</span><span class="nam">__dict__</span> <span class="op">==</span> <span class="nam">other</span><span class="op">.</span><span class="nam">__dict__</span><span class="strut">&nbsp;</span></p>
+<p id="t237" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t238" class="stm run hide_run">    <span class="key">def</span> <span class="nam">clone</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t239" class="pln">        <span class="str">""" Make a clone of these options, for further refinement.</span><span class="strut">&nbsp;</span></p>
+<p id="t240" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
+<p id="t241" class="stm mis">        <span class="key">return</span> <span class="nam">copy</span><span class="op">.</span><span class="nam">deepcopy</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t242" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t243" class="stm run hide_run">    <span class="key">def</span> <span class="nam">addToIncludePath</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">dirs</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t244" class="pln">        <span class="str">""" Add directories to the include path.</span><span class="strut">&nbsp;</span></p>
+<p id="t245" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
+<p id="t246" class="stm mis">        <span class="nam">dirs</span> <span class="op">=</span> <span class="nam">dirs</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="nam">os</span><span class="op">.</span><span class="nam">pathsep</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t247" class="stm mis">        <span class="nam">self</span><span class="op">.</span><span class="nam">includePath</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="nam">dirs</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t248" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t249" class="stm run hide_run">    <span class="key">def</span> <span class="nam">parseArgs</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">argv</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t250" class="pln">        <span class="com"># Parse the command line arguments.</span><span class="strut">&nbsp;</span></p>
+<p id="t251" class="stm mis">        <span class="key">try</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t252" class="stm mis">            <span class="nam">opts</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">args</span> <span class="op">=</span> <span class="nam">getopt</span><span class="op">.</span><span class="nam">getopt</span><span class="op">(</span><span class="strut">&nbsp;</span></p>
+<p id="t253" class="pln">                <span class="nam">argv</span><span class="op">,</span><span class="strut">&nbsp;</span></p>
+<p id="t254" class="pln">                <span class="str">'cdD:eI:n:o:rs:Uvw:xz'</span><span class="op">,</span><span class="strut">&nbsp;</span></p>
+<p id="t255" class="pln">                <span class="op">[</span><span class="strut">&nbsp;</span></p>
+<p id="t256" class="pln">                    <span class="str">'markers='</span><span class="op">,</span><span class="strut">&nbsp;</span></p>
+<p id="t257" class="pln">                    <span class="str">'verbosity='</span><span class="op">,</span><span class="strut">&nbsp;</span></p>
+<p id="t258" class="pln">                <span class="op">]</span><span class="strut">&nbsp;</span></p>
+<p id="t259" class="pln">            <span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t260" class="stm mis">        <span class="key">except</span> <span class="nam">getopt</span><span class="op">.</span><span class="nam">error</span> <span class="key">as</span> <span class="nam">msg</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t261" class="stm mis">            <span class="key">raise</span> <span class="nam">CogUsageError</span><span class="op">(</span><span class="nam">msg</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t262" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t263" class="pln">        <span class="com"># Handle the command line arguments.</span><span class="strut">&nbsp;</span></p>
+<p id="t264" class="stm mis">        <span class="key">for</span> <span class="nam">o</span><span class="op">,</span> <span class="nam">a</span> <span class="key">in</span> <span class="nam">opts</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t265" class="stm mis">            <span class="key">if</span> <span class="nam">o</span> <span class="op">==</span> <span class="str">'-c'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t266" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">bHashOutput</span> <span class="op">=</span> <span class="nam">True</span><span class="strut">&nbsp;</span></p>
+<p id="t267" class="stm mis">            <span class="key">elif</span> <span class="nam">o</span> <span class="op">==</span> <span class="str">'-d'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t268" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">bDeleteCode</span> <span class="op">=</span> <span class="nam">True</span><span class="strut">&nbsp;</span></p>
+<p id="t269" class="stm mis">            <span class="key">elif</span> <span class="nam">o</span> <span class="op">==</span> <span class="str">'-D'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t270" class="stm mis">                <span class="key">if</span> <span class="nam">a</span><span class="op">.</span><span class="nam">count</span><span class="op">(</span><span class="str">'='</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">1</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t271" class="stm mis">                    <span class="key">raise</span> <span class="nam">CogUsageError</span><span class="op">(</span><span class="str">"-D takes a name=value argument"</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t272" class="stm mis">                <span class="nam">name</span><span class="op">,</span> <span class="nam">value</span> <span class="op">=</span> <span class="nam">a</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="str">'='</span><span class="op">,</span> <span class="num">1</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t273" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">defines</span><span class="op">[</span><span class="nam">name</span><span class="op">]</span> <span class="op">=</span> <span class="nam">value</span><span class="strut">&nbsp;</span></p>
+<p id="t274" class="stm mis">            <span class="key">elif</span> <span class="nam">o</span> <span class="op">==</span> <span class="str">'-e'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t275" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">bWarnEmpty</span> <span class="op">=</span> <span class="nam">True</span><span class="strut">&nbsp;</span></p>
+<p id="t276" class="stm mis">            <span class="key">elif</span> <span class="nam">o</span> <span class="op">==</span> <span class="str">'-I'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t277" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">addToIncludePath</span><span class="op">(</span><span class="nam">a</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t278" class="stm mis">            <span class="key">elif</span> <span class="nam">o</span> <span class="op">==</span> <span class="str">'-n'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t279" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">sEncoding</span> <span class="op">=</span> <span class="nam">a</span><span class="strut">&nbsp;</span></p>
+<p id="t280" class="stm mis">            <span class="key">elif</span> <span class="nam">o</span> <span class="op">==</span> <span class="str">'-o'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t281" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">sOutputName</span> <span class="op">=</span> <span class="nam">a</span><span class="strut">&nbsp;</span></p>
+<p id="t282" class="stm mis">            <span class="key">elif</span> <span class="nam">o</span> <span class="op">==</span> <span class="str">'-r'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t283" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">bReplace</span> <span class="op">=</span> <span class="nam">True</span><span class="strut">&nbsp;</span></p>
+<p id="t284" class="stm mis">            <span class="key">elif</span> <span class="nam">o</span> <span class="op">==</span> <span class="str">'-s'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t285" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">sSuffix</span> <span class="op">=</span> <span class="nam">a</span><span class="strut">&nbsp;</span></p>
+<p id="t286" class="stm mis">            <span class="key">elif</span> <span class="nam">o</span> <span class="op">==</span> <span class="str">'-U'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t287" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">bNewlines</span> <span class="op">=</span> <span class="nam">True</span><span class="strut">&nbsp;</span></p>
+<p id="t288" class="stm mis">            <span class="key">elif</span> <span class="nam">o</span> <span class="op">==</span> <span class="str">'-v'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t289" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">bShowVersion</span> <span class="op">=</span> <span class="nam">True</span><span class="strut">&nbsp;</span></p>
+<p id="t290" class="stm mis">            <span class="key">elif</span> <span class="nam">o</span> <span class="op">==</span> <span class="str">'-w'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t291" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">sMakeWritableCmd</span> <span class="op">=</span> <span class="nam">a</span><span class="strut">&nbsp;</span></p>
+<p id="t292" class="stm mis">            <span class="key">elif</span> <span class="nam">o</span> <span class="op">==</span> <span class="str">'-x'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t293" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">bNoGenerate</span> <span class="op">=</span> <span class="nam">True</span><span class="strut">&nbsp;</span></p>
+<p id="t294" class="stm mis">            <span class="key">elif</span> <span class="nam">o</span> <span class="op">==</span> <span class="str">'-z'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t295" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">bEofCanBeEnd</span> <span class="op">=</span> <span class="nam">True</span><span class="strut">&nbsp;</span></p>
+<p id="t296" class="stm mis">            <span class="key">elif</span> <span class="nam">o</span> <span class="op">==</span> <span class="str">'--markers'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t297" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">_parse_markers</span><span class="op">(</span><span class="nam">a</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t298" class="stm mis">            <span class="key">elif</span> <span class="nam">o</span> <span class="op">==</span> <span class="str">'--verbosity'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t299" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">verbosity</span> <span class="op">=</span> <span class="nam">int</span><span class="op">(</span><span class="nam">a</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t300" class="pln">            <span class="key">else</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t301" class="pln">                <span class="com"># Since getopt.getopt is given a list of possible flags,</span><span class="strut">&nbsp;</span></p>
+<p id="t302" class="pln">                <span class="com"># this is an internal error.</span><span class="strut">&nbsp;</span></p>
+<p id="t303" class="exc">                <span class="key">raise</span> <span class="nam">CogInternalError</span><span class="op">(</span><span class="str">"Don't understand argument %s"</span> <span class="op">%</span> <span class="nam">o</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t304" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t305" class="stm run hide_run">    <span class="key">def</span> <span class="nam">_parse_markers</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">val</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t306" class="stm mis">        <span class="key">try</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t307" class="stm mis">            <span class="nam">self</span><span class="op">.</span><span class="nam">sBeginSpec</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sEndSpec</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sEndOutput</span> <span class="op">=</span> <span class="nam">val</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="str">' '</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t308" class="stm mis">        <span class="key">except</span> <span class="nam">ValueError</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t309" class="stm mis">            <span class="key">raise</span> <span class="nam">CogUsageError</span><span class="op">(</span><span class="strut">&nbsp;</span></p>
+<p id="t310" class="pln">                <span class="str">'--markers requires 3 values separated by spaces, could not parse %r'</span> <span class="op">%</span> <span class="nam">val</span><span class="strut">&nbsp;</span></p>
+<p id="t311" class="pln">            <span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t312" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t313" class="stm run hide_run">    <span class="key">def</span> <span class="nam">validate</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t314" class="pln">        <span class="str">""" Does nothing if everything is OK, raises CogError's if it's not.</span><span class="strut">&nbsp;</span></p>
+<p id="t315" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
+<p id="t316" class="stm mis">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">bReplace</span> <span class="key">and</span> <span class="nam">self</span><span class="op">.</span><span class="nam">bDeleteCode</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t317" class="stm mis">            <span class="key">raise</span> <span class="nam">CogUsageError</span><span class="op">(</span><span class="str">"Can't use -d with -r (or you would delete all your source!)"</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t318" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t319" class="stm mis">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">bReplace</span> <span class="key">and</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sOutputName</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t320" class="stm mis">            <span class="key">raise</span> <span class="nam">CogUsageError</span><span class="op">(</span><span class="str">"Can't use -o with -r (they are opposites)"</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t321" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t322" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t323" class="stm run hide_run"><span class="key">class</span> <span class="nam">Cog</span><span class="op">(</span><span class="nam">Redirectable</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t324" class="pln">    <span class="str">""" The Cog engine.</span><span class="strut">&nbsp;</span></p>
+<p id="t325" class="pln"><span class="str">    """</span><span class="strut">&nbsp;</span></p>
+<p id="t326" class="stm run hide_run">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t327" class="stm run hide_run">        <span class="nam">Redirectable</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t328" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">options</span> <span class="op">=</span> <span class="nam">CogOptions</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t329" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">_fixEndOutputPatterns</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t330" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">installCogModule</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t331" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t332" class="stm run hide_run">    <span class="key">def</span> <span class="nam">_fixEndOutputPatterns</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t333" class="stm run hide_run">        <span class="nam">end_output</span> <span class="op">=</span> <span class="nam">re</span><span class="op">.</span><span class="nam">escape</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sEndOutput</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t334" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">reEndOutput</span> <span class="op">=</span> <span class="nam">re</span><span class="op">.</span><span class="nam">compile</span><span class="op">(</span><span class="nam">end_output</span> <span class="op">+</span> <span class="str">r'(?P&lt;hashsect> *\(checksum: (?P&lt;hash>[a-f0-9]+)\))'</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t335" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">sEndFormat</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sEndOutput</span> <span class="op">+</span> <span class="str">' (checksum: %s)'</span><span class="strut">&nbsp;</span></p>
+<p id="t336" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t337" class="stm run hide_run">    <span class="key">def</span> <span class="nam">showWarning</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">msg</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t338" class="stm mis">        <span class="nam">self</span><span class="op">.</span><span class="nam">prout</span><span class="op">(</span><span class="str">"Warning: "</span><span class="op">+</span><span class="nam">msg</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t339" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t340" class="stm run hide_run">    <span class="key">def</span> <span class="nam">isBeginSpecLine</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">s</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t341" class="stm run hide_run">        <span class="key">return</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sBeginSpec</span> <span class="key">in</span> <span class="nam">s</span><span class="strut">&nbsp;</span></p>
+<p id="t342" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t343" class="stm run hide_run">    <span class="key">def</span> <span class="nam">isEndSpecLine</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">s</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t344" class="stm run hide_run">        <span class="key">return</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sEndSpec</span> <span class="key">in</span> <span class="nam">s</span> <span class="key">and</span> <span class="key">not</span> <span class="nam">self</span><span class="op">.</span><span class="nam">isEndOutputLine</span><span class="op">(</span><span class="nam">s</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t345" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t346" class="stm run hide_run">    <span class="key">def</span> <span class="nam">isEndOutputLine</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">s</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t347" class="stm run hide_run">        <span class="key">return</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sEndOutput</span> <span class="key">in</span> <span class="nam">s</span><span class="strut">&nbsp;</span></p>
+<p id="t348" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t349" class="stm run hide_run">    <span class="key">def</span> <span class="nam">installCogModule</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t350" class="pln">        <span class="str">""" Magic mumbo-jumbo so that imported Python modules</span><span class="strut">&nbsp;</span></p>
+<p id="t351" class="pln"><span class="str">            can say "import cog" and get our state.</span><span class="strut">&nbsp;</span></p>
+<p id="t352" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
+<p id="t353" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">cogmodule</span> <span class="op">=</span> <span class="nam">imp</span><span class="op">.</span><span class="nam">new_module</span><span class="op">(</span><span class="str">'cog'</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t354" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">cogmodule</span><span class="op">.</span><span class="nam">path</span> <span class="op">=</span> <span class="op">[</span><span class="op">]</span><span class="strut">&nbsp;</span></p>
+<p id="t355" class="stm run hide_run">        <span class="nam">sys</span><span class="op">.</span><span class="nam">modules</span><span class="op">[</span><span class="str">'cog'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">cogmodule</span><span class="strut">&nbsp;</span></p>
+<p id="t356" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t357" class="stm run hide_run">    <span class="key">def</span> <span class="nam">openOutputFile</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">fname</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t358" class="pln">        <span class="str">""" Open an output file, taking all the details into account.</span><span class="strut">&nbsp;</span></p>
+<p id="t359" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
+<p id="t360" class="stm mis">        <span class="nam">opts</span> <span class="op">=</span> <span class="op">{</span><span class="op">}</span><span class="strut">&nbsp;</span></p>
+<p id="t361" class="stm mis">        <span class="nam">mode</span> <span class="op">=</span> <span class="str">"w"</span><span class="strut">&nbsp;</span></p>
+<p id="t362" class="stm mis">        <span class="key">if</span> <span class="nam">PY3</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t363" class="stm mis">            <span class="nam">opts</span><span class="op">[</span><span class="str">'encoding'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sEncoding</span><span class="strut">&nbsp;</span></p>
+<p id="t364" class="stm mis">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">bNewlines</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t365" class="stm mis">            <span class="key">if</span> <span class="nam">PY3</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t366" class="stm mis">                <span class="nam">opts</span><span class="op">[</span><span class="str">'newline'</span><span class="op">]</span> <span class="op">=</span> <span class="str">"\n"</span><span class="strut">&nbsp;</span></p>
+<p id="t367" class="pln">            <span class="key">else</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t368" class="stm mis">                <span class="nam">mode</span> <span class="op">=</span> <span class="str">"wb"</span><span class="strut">&nbsp;</span></p>
+<p id="t369" class="stm mis">        <span class="nam">fdir</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">dirname</span><span class="op">(</span><span class="nam">fname</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t370" class="stm mis">        <span class="key">if</span> <span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">dirname</span><span class="op">(</span><span class="nam">fdir</span><span class="op">)</span> <span class="key">and</span> <span class="key">not</span> <span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">exists</span><span class="op">(</span><span class="nam">fdir</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t371" class="stm mis">            <span class="nam">os</span><span class="op">.</span><span class="nam">makedirs</span><span class="op">(</span><span class="nam">fdir</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t372" class="stm mis">        <span class="key">return</span> <span class="nam">open</span><span class="op">(</span><span class="nam">fname</span><span class="op">,</span> <span class="nam">mode</span><span class="op">,</span> <span class="op">**</span><span class="nam">opts</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t373" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t374" class="stm run hide_run">    <span class="key">def</span> <span class="nam">openInputFile</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">fname</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t375" class="pln">        <span class="str">""" Open an input file. """</span><span class="strut">&nbsp;</span></p>
+<p id="t376" class="stm mis">        <span class="key">if</span> <span class="nam">fname</span> <span class="op">==</span> <span class="str">"-"</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t377" class="stm mis">            <span class="key">return</span> <span class="nam">sys</span><span class="op">.</span><span class="nam">stdin</span><span class="strut">&nbsp;</span></p>
+<p id="t378" class="pln">        <span class="key">else</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t379" class="stm mis">            <span class="nam">opts</span> <span class="op">=</span> <span class="op">{</span><span class="op">}</span><span class="strut">&nbsp;</span></p>
+<p id="t380" class="stm mis">            <span class="key">if</span> <span class="nam">PY3</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t381" class="stm mis">                <span class="nam">opts</span><span class="op">[</span><span class="str">'encoding'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sEncoding</span><span class="strut">&nbsp;</span></p>
+<p id="t382" class="stm mis">            <span class="key">return</span> <span class="nam">open</span><span class="op">(</span><span class="nam">fname</span><span class="op">,</span> <span class="str">"r"</span><span class="op">,</span> <span class="op">**</span><span class="nam">opts</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t383" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t384" class="stm run hide_run">    <span class="key">def</span> <span class="nam">processFile</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">fIn</span><span class="op">,</span> <span class="nam">fOut</span><span class="op">,</span> <span class="nam">fname</span><span class="op">=</span><span class="nam">None</span><span class="op">,</span> <span class="nam">globals</span><span class="op">=</span><span class="nam">None</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t385" class="pln">        <span class="str">""" Process an input file object to an output file object.</span><span class="strut">&nbsp;</span></p>
+<p id="t386" class="pln"><span class="str">            fIn and fOut can be file objects, or file names.</span><span class="strut">&nbsp;</span></p>
+<p id="t387" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
+<p id="t388" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t389" class="stm run hide_run">        <span class="nam">sFileIn</span> <span class="op">=</span> <span class="nam">fname</span> <span class="key">or</span> <span class="str">''</span><span class="strut">&nbsp;</span></p>
+<p id="t390" class="stm run hide_run">        <span class="nam">sFileOut</span> <span class="op">=</span> <span class="nam">fname</span> <span class="key">or</span> <span class="str">''</span><span class="strut">&nbsp;</span></p>
+<p id="t391" class="stm run hide_run">        <span class="nam">fInToClose</span> <span class="op">=</span> <span class="nam">fOutToClose</span> <span class="op">=</span> <span class="nam">None</span><span class="strut">&nbsp;</span></p>
+<p id="t392" class="pln">        <span class="com"># Convert filenames to files.</span><span class="strut">&nbsp;</span></p>
+<p id="t393" class="stm par run hide_run"><span class="annotate short">393&#x202F;&#x219B;&#x202F;395</span><span class="annotate long">line 393 didn't jump to line 395, because the condition on line 393 was never true</span>        <span class="key">if</span> <span class="nam">isinstance</span><span class="op">(</span><span class="nam">fIn</span><span class="op">,</span> <span class="nam">string_types</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t394" class="pln">            <span class="com"># Open the input file.</span><span class="strut">&nbsp;</span></p>
+<p id="t395" class="stm mis">            <span class="nam">sFileIn</span> <span class="op">=</span> <span class="nam">fIn</span><span class="strut">&nbsp;</span></p>
+<p id="t396" class="stm mis">            <span class="nam">fIn</span> <span class="op">=</span> <span class="nam">fInToClose</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">openInputFile</span><span class="op">(</span><span class="nam">fIn</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t397" class="stm par run hide_run"><span class="annotate short">397&#x202F;&#x219B;&#x202F;399</span><span class="annotate long">line 397 didn't jump to line 399, because the condition on line 397 was never true</span>        <span class="key">if</span> <span class="nam">isinstance</span><span class="op">(</span><span class="nam">fOut</span><span class="op">,</span> <span class="nam">string_types</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t398" class="pln">            <span class="com"># Open the output file.</span><span class="strut">&nbsp;</span></p>
+<p id="t399" class="stm mis">            <span class="nam">sFileOut</span> <span class="op">=</span> <span class="nam">fOut</span><span class="strut">&nbsp;</span></p>
+<p id="t400" class="stm mis">            <span class="nam">fOut</span> <span class="op">=</span> <span class="nam">fOutToClose</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">openOutputFile</span><span class="op">(</span><span class="nam">fOut</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t401" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t402" class="stm run hide_run">        <span class="key">try</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t403" class="stm run hide_run">            <span class="nam">fIn</span> <span class="op">=</span> <span class="nam">NumberedFileReader</span><span class="op">(</span><span class="nam">fIn</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
 <p id="t404" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t405" class="stm run hide_run">            <span class="nam">self</span><span class="op">.</span><span class="nam">cogmodule</span><span class="op">.</span><span class="nam">inFile</span> <span class="op">=</span> <span class="nam">sFileIn</span><span class="strut">&nbsp;</span></p>
-<p id="t406" class="stm run hide_run">            <span class="nam">self</span><span class="op">.</span><span class="nam">cogmodule</span><span class="op">.</span><span class="nam">outFile</span> <span class="op">=</span> <span class="nam">sFileOut</span><span class="strut">&nbsp;</span></p>
-<p id="t407" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t408" class="pln">            <span class="com"># The globals dict we'll use for this file.</span><span class="strut">&nbsp;</span></p>
-<p id="t409" class="stm par run hide_run"><span class="annotate short">409&#x202F;&#x219B;&#x202F;413</span><span class="annotate long">line 409 didn't jump to line 413, because the condition on line 409 was never false</span>            <span class="key">if</span> <span class="nam">globals</span> <span class="key">is</span> <span class="nam">None</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t410" class="stm run hide_run">                <span class="nam">globals</span> <span class="op">=</span> <span class="op">{</span><span class="op">}</span><span class="strut">&nbsp;</span></p>
-<p id="t411" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t412" class="pln">            <span class="com"># If there are any global defines, put them in the globals.</span><span class="strut">&nbsp;</span></p>
-<p id="t413" class="stm run hide_run">            <span class="nam">globals</span><span class="op">.</span><span class="nam">update</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">defines</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t414" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t415" class="pln">            <span class="com"># loop over generator chunks</span><span class="strut">&nbsp;</span></p>
-<p id="t416" class="stm run hide_run">            <span class="nam">l</span> <span class="op">=</span> <span class="nam">fIn</span><span class="op">.</span><span class="nam">readline</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t417" class="stm run hide_run">            <span class="key">while</span> <span class="nam">l</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t418" class="pln">                <span class="com"># Find the next spec begin</span><span class="strut">&nbsp;</span></p>
-<p id="t419" class="stm run hide_run">                <span class="key">while</span> <span class="nam">l</span> <span class="key">and</span> <span class="key">not</span> <span class="nam">self</span><span class="op">.</span><span class="nam">isBeginSpecLine</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t420" class="stm par run hide_run"><span class="annotate short">420&#x202F;&#x219B;&#x202F;421</span><span class="annotate long">line 420 didn't jump to line 421, because the condition on line 420 was never true</span>                    <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">isEndSpecLine</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t421" class="stm mis">                        <span class="key">raise</span> <span class="nam">CogError</span><span class="op">(</span><span class="str">"Unexpected '%s'"</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sEndSpec</span><span class="op">,</span><span class="strut">&nbsp;</span></p>
-<p id="t422" class="pln">                            <span class="nam">file</span><span class="op">=</span><span class="nam">sFileIn</span><span class="op">,</span> <span class="nam">line</span><span class="op">=</span><span class="nam">fIn</span><span class="op">.</span><span class="nam">linenumber</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t423" class="stm par run hide_run"><span class="annotate short">423&#x202F;&#x219B;&#x202F;424</span><span class="annotate long">line 423 didn't jump to line 424, because the condition on line 423 was never true</span>                    <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">isEndOutputLine</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t424" class="stm mis">                        <span class="key">raise</span> <span class="nam">CogError</span><span class="op">(</span><span class="str">"Unexpected '%s'"</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sEndOutput</span><span class="op">,</span><span class="strut">&nbsp;</span></p>
-<p id="t425" class="pln">                            <span class="nam">file</span><span class="op">=</span><span class="nam">sFileIn</span><span class="op">,</span> <span class="nam">line</span><span class="op">=</span><span class="nam">fIn</span><span class="op">.</span><span class="nam">linenumber</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t426" class="stm run hide_run">                    <span class="nam">fOut</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t427" class="stm run hide_run">                    <span class="nam">l</span> <span class="op">=</span> <span class="nam">fIn</span><span class="op">.</span><span class="nam">readline</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t428" class="stm run hide_run">                <span class="key">if</span> <span class="key">not</span> <span class="nam">l</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t429" class="stm run hide_run">                    <span class="key">break</span><span class="strut">&nbsp;</span></p>
-<p id="t430" class="stm par run hide_run"><span class="annotate short">430&#x202F;&#x219B;&#x202F;434</span><span class="annotate long">line 430 didn't jump to line 434, because the condition on line 430 was never false</span>                <span class="key">if</span> <span class="key">not</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">bDeleteCode</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t431" class="stm run hide_run">                    <span class="nam">fOut</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t432" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t433" class="pln">                <span class="com"># l is the begin spec</span><span class="strut">&nbsp;</span></p>
-<p id="t434" class="stm run hide_run">                <span class="nam">gen</span> <span class="op">=</span> <span class="nam">CogGenerator</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t435" class="stm run hide_run">                <span class="nam">gen</span><span class="op">.</span><span class="nam">setOutput</span><span class="op">(</span><span class="nam">stdout</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">stdout</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t436" class="stm run hide_run">                <span class="nam">gen</span><span class="op">.</span><span class="nam">parseMarker</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t437" class="stm run hide_run">                <span class="nam">firstLineNum</span> <span class="op">=</span> <span class="nam">fIn</span><span class="op">.</span><span class="nam">linenumber</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t438" class="stm run hide_run">                <span class="nam">self</span><span class="op">.</span><span class="nam">cogmodule</span><span class="op">.</span><span class="nam">firstLineNum</span> <span class="op">=</span> <span class="nam">firstLineNum</span><span class="strut">&nbsp;</span></p>
-<p id="t439" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t440" class="pln">                <span class="com"># If the spec begin is also a spec end, then process the single</span><span class="strut">&nbsp;</span></p>
-<p id="t441" class="pln">                <span class="com"># line of code inside.</span><span class="strut">&nbsp;</span></p>
-<p id="t442" class="stm run hide_run">                <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">isEndSpecLine</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t443" class="stm run hide_run">                    <span class="nam">beg</span> <span class="op">=</span> <span class="nam">l</span><span class="op">.</span><span class="nam">find</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sBeginSpec</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t444" class="stm run hide_run">                    <span class="nam">end</span> <span class="op">=</span> <span class="nam">l</span><span class="op">.</span><span class="nam">find</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sEndSpec</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t445" class="stm run hide_run">                    <span class="key">if</span> <span class="nam">beg</span> <span class="op">></span> <span class="nam">end</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t446" class="stm run hide_run">                        <span class="key">raise</span> <span class="nam">CogError</span><span class="op">(</span><span class="str">"Cog code markers inverted"</span><span class="op">,</span><span class="strut">&nbsp;</span></p>
-<p id="t447" class="pln">                            <span class="nam">file</span><span class="op">=</span><span class="nam">sFileIn</span><span class="op">,</span> <span class="nam">line</span><span class="op">=</span><span class="nam">firstLineNum</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t448" class="pln">                    <span class="key">else</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t449" class="stm run hide_run">                        <span class="nam">sCode</span> <span class="op">=</span> <span class="nam">l</span><span class="op">[</span><span class="nam">beg</span><span class="op">+</span><span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sBeginSpec</span><span class="op">)</span><span class="op">:</span><span class="nam">end</span><span class="op">]</span><span class="op">.</span><span class="nam">strip</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t450" class="stm run hide_run">                        <span class="nam">gen</span><span class="op">.</span><span class="nam">parseLine</span><span class="op">(</span><span class="nam">sCode</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t451" class="pln">                <span class="key">else</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t452" class="pln">                    <span class="com"># Deal with an ordinary code block.</span><span class="strut">&nbsp;</span></p>
-<p id="t453" class="stm run hide_run">                    <span class="nam">l</span> <span class="op">=</span> <span class="nam">fIn</span><span class="op">.</span><span class="nam">readline</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t454" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t455" class="pln">                    <span class="com"># Get all the lines in the spec</span><span class="strut">&nbsp;</span></p>
-<p id="t456" class="stm run hide_run">                    <span class="key">while</span> <span class="nam">l</span> <span class="key">and</span> <span class="key">not</span> <span class="nam">self</span><span class="op">.</span><span class="nam">isEndSpecLine</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t457" class="stm par run hide_run"><span class="annotate short">457&#x202F;&#x219B;&#x202F;458</span><span class="annotate long">line 457 didn't jump to line 458, because the condition on line 457 was never true</span>                        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">isBeginSpecLine</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t458" class="stm mis">                            <span class="key">raise</span> <span class="nam">CogError</span><span class="op">(</span><span class="str">"Unexpected '%s'"</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sBeginSpec</span><span class="op">,</span><span class="strut">&nbsp;</span></p>
-<p id="t459" class="pln">                                <span class="nam">file</span><span class="op">=</span><span class="nam">sFileIn</span><span class="op">,</span> <span class="nam">line</span><span class="op">=</span><span class="nam">fIn</span><span class="op">.</span><span class="nam">linenumber</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t460" class="stm par run hide_run"><span class="annotate short">460&#x202F;&#x219B;&#x202F;461</span><span class="annotate long">line 460 didn't jump to line 461, because the condition on line 460 was never true</span>                        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">isEndOutputLine</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t461" class="stm mis">                            <span class="key">raise</span> <span class="nam">CogError</span><span class="op">(</span><span class="str">"Unexpected '%s'"</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sEndOutput</span><span class="op">,</span><span class="strut">&nbsp;</span></p>
-<p id="t462" class="pln">                                <span class="nam">file</span><span class="op">=</span><span class="nam">sFileIn</span><span class="op">,</span> <span class="nam">line</span><span class="op">=</span><span class="nam">fIn</span><span class="op">.</span><span class="nam">linenumber</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t463" class="stm par run hide_run"><span class="annotate short">463&#x202F;&#x219B;&#x202F;465</span><span class="annotate long">line 463 didn't jump to line 465, because the condition on line 463 was never false</span>                        <span class="key">if</span> <span class="key">not</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">bDeleteCode</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t464" class="stm run hide_run">                            <span class="nam">fOut</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t465" class="stm run hide_run">                        <span class="nam">gen</span><span class="op">.</span><span class="nam">parseLine</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t466" class="stm run hide_run">                        <span class="nam">l</span> <span class="op">=</span> <span class="nam">fIn</span><span class="op">.</span><span class="nam">readline</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t467" class="stm par run hide_run"><span class="annotate short">467&#x202F;&#x219B;&#x202F;468</span><span class="annotate long">line 467 didn't jump to line 468, because the condition on line 467 was never true</span>                    <span class="key">if</span> <span class="key">not</span> <span class="nam">l</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t468" class="stm mis">                        <span class="key">raise</span> <span class="nam">CogError</span><span class="op">(</span><span class="strut">&nbsp;</span></p>
-<p id="t469" class="pln">                            <span class="str">"Cog block begun but never ended."</span><span class="op">,</span><span class="strut">&nbsp;</span></p>
-<p id="t470" class="pln">                            <span class="nam">file</span><span class="op">=</span><span class="nam">sFileIn</span><span class="op">,</span> <span class="nam">line</span><span class="op">=</span><span class="nam">firstLineNum</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t471" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t472" class="stm par run hide_run"><span class="annotate short">472&#x202F;&#x219B;&#x202F;474</span><span class="annotate long">line 472 didn't jump to line 474, because the condition on line 472 was never false</span>                    <span class="key">if</span> <span class="key">not</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">bDeleteCode</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t473" class="stm run hide_run">                        <span class="nam">fOut</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t474" class="stm run hide_run">                    <span class="nam">gen</span><span class="op">.</span><span class="nam">parseMarker</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t475" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t476" class="stm run hide_run">                <span class="nam">l</span> <span class="op">=</span> <span class="nam">fIn</span><span class="op">.</span><span class="nam">readline</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t405" class="stm run hide_run">            <span class="nam">bSawCog</span> <span class="op">=</span> <span class="nam">False</span><span class="strut">&nbsp;</span></p>
+<p id="t406" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t407" class="stm run hide_run">            <span class="nam">self</span><span class="op">.</span><span class="nam">cogmodule</span><span class="op">.</span><span class="nam">inFile</span> <span class="op">=</span> <span class="nam">sFileIn</span><span class="strut">&nbsp;</span></p>
+<p id="t408" class="stm run hide_run">            <span class="nam">self</span><span class="op">.</span><span class="nam">cogmodule</span><span class="op">.</span><span class="nam">outFile</span> <span class="op">=</span> <span class="nam">sFileOut</span><span class="strut">&nbsp;</span></p>
+<p id="t409" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t410" class="pln">            <span class="com"># The globals dict we'll use for this file.</span><span class="strut">&nbsp;</span></p>
+<p id="t411" class="stm par run hide_run"><span class="annotate short">411&#x202F;&#x219B;&#x202F;415</span><span class="annotate long">line 411 didn't jump to line 415, because the condition on line 411 was never false</span>            <span class="key">if</span> <span class="nam">globals</span> <span class="key">is</span> <span class="nam">None</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t412" class="stm run hide_run">                <span class="nam">globals</span> <span class="op">=</span> <span class="op">{</span><span class="op">}</span><span class="strut">&nbsp;</span></p>
+<p id="t413" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t414" class="pln">            <span class="com"># If there are any global defines, put them in the globals.</span><span class="strut">&nbsp;</span></p>
+<p id="t415" class="stm run hide_run">            <span class="nam">globals</span><span class="op">.</span><span class="nam">update</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">defines</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t416" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t417" class="pln">            <span class="com"># loop over generator chunks</span><span class="strut">&nbsp;</span></p>
+<p id="t418" class="stm run hide_run">            <span class="nam">l</span> <span class="op">=</span> <span class="nam">fIn</span><span class="op">.</span><span class="nam">readline</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t419" class="stm run hide_run">            <span class="key">while</span> <span class="nam">l</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t420" class="pln">                <span class="com"># Find the next spec begin</span><span class="strut">&nbsp;</span></p>
+<p id="t421" class="stm run hide_run">                <span class="key">while</span> <span class="nam">l</span> <span class="key">and</span> <span class="key">not</span> <span class="nam">self</span><span class="op">.</span><span class="nam">isBeginSpecLine</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t422" class="stm par run hide_run"><span class="annotate short">422&#x202F;&#x219B;&#x202F;423</span><span class="annotate long">line 422 didn't jump to line 423, because the condition on line 422 was never true</span>                    <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">isEndSpecLine</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t423" class="stm mis">                        <span class="key">raise</span> <span class="nam">CogError</span><span class="op">(</span><span class="str">"Unexpected '%s'"</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sEndSpec</span><span class="op">,</span><span class="strut">&nbsp;</span></p>
+<p id="t424" class="pln">                            <span class="nam">file</span><span class="op">=</span><span class="nam">sFileIn</span><span class="op">,</span> <span class="nam">line</span><span class="op">=</span><span class="nam">fIn</span><span class="op">.</span><span class="nam">linenumber</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t425" class="stm par run hide_run"><span class="annotate short">425&#x202F;&#x219B;&#x202F;426</span><span class="annotate long">line 425 didn't jump to line 426, because the condition on line 425 was never true</span>                    <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">isEndOutputLine</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t426" class="stm mis">                        <span class="key">raise</span> <span class="nam">CogError</span><span class="op">(</span><span class="str">"Unexpected '%s'"</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sEndOutput</span><span class="op">,</span><span class="strut">&nbsp;</span></p>
+<p id="t427" class="pln">                            <span class="nam">file</span><span class="op">=</span><span class="nam">sFileIn</span><span class="op">,</span> <span class="nam">line</span><span class="op">=</span><span class="nam">fIn</span><span class="op">.</span><span class="nam">linenumber</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t428" class="stm run hide_run">                    <span class="nam">fOut</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t429" class="stm run hide_run">                    <span class="nam">l</span> <span class="op">=</span> <span class="nam">fIn</span><span class="op">.</span><span class="nam">readline</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t430" class="stm run hide_run">                <span class="key">if</span> <span class="key">not</span> <span class="nam">l</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t431" class="stm run hide_run">                    <span class="key">break</span><span class="strut">&nbsp;</span></p>
+<p id="t432" class="stm par run hide_run"><span class="annotate short">432&#x202F;&#x219B;&#x202F;436</span><span class="annotate long">line 432 didn't jump to line 436, because the condition on line 432 was never false</span>                <span class="key">if</span> <span class="key">not</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">bDeleteCode</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t433" class="stm run hide_run">                    <span class="nam">fOut</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t434" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t435" class="pln">                <span class="com"># l is the begin spec</span><span class="strut">&nbsp;</span></p>
+<p id="t436" class="stm run hide_run">                <span class="nam">gen</span> <span class="op">=</span> <span class="nam">CogGenerator</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t437" class="stm run hide_run">                <span class="nam">gen</span><span class="op">.</span><span class="nam">setOutput</span><span class="op">(</span><span class="nam">stdout</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">stdout</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t438" class="stm run hide_run">                <span class="nam">gen</span><span class="op">.</span><span class="nam">parseMarker</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t439" class="stm run hide_run">                <span class="nam">firstLineNum</span> <span class="op">=</span> <span class="nam">fIn</span><span class="op">.</span><span class="nam">linenumber</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t440" class="stm run hide_run">                <span class="nam">self</span><span class="op">.</span><span class="nam">cogmodule</span><span class="op">.</span><span class="nam">firstLineNum</span> <span class="op">=</span> <span class="nam">firstLineNum</span><span class="strut">&nbsp;</span></p>
+<p id="t441" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t442" class="pln">                <span class="com"># If the spec begin is also a spec end, then process the single</span><span class="strut">&nbsp;</span></p>
+<p id="t443" class="pln">                <span class="com"># line of code inside.</span><span class="strut">&nbsp;</span></p>
+<p id="t444" class="stm run hide_run">                <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">isEndSpecLine</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t445" class="stm run hide_run">                    <span class="nam">beg</span> <span class="op">=</span> <span class="nam">l</span><span class="op">.</span><span class="nam">find</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sBeginSpec</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t446" class="stm run hide_run">                    <span class="nam">end</span> <span class="op">=</span> <span class="nam">l</span><span class="op">.</span><span class="nam">find</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sEndSpec</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t447" class="stm run hide_run">                    <span class="key">if</span> <span class="nam">beg</span> <span class="op">></span> <span class="nam">end</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t448" class="stm run hide_run">                        <span class="key">raise</span> <span class="nam">CogError</span><span class="op">(</span><span class="str">"Cog code markers inverted"</span><span class="op">,</span><span class="strut">&nbsp;</span></p>
+<p id="t449" class="pln">                            <span class="nam">file</span><span class="op">=</span><span class="nam">sFileIn</span><span class="op">,</span> <span class="nam">line</span><span class="op">=</span><span class="nam">firstLineNum</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t450" class="pln">                    <span class="key">else</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t451" class="stm run hide_run">                        <span class="nam">sCode</span> <span class="op">=</span> <span class="nam">l</span><span class="op">[</span><span class="nam">beg</span><span class="op">+</span><span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sBeginSpec</span><span class="op">)</span><span class="op">:</span><span class="nam">end</span><span class="op">]</span><span class="op">.</span><span class="nam">strip</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t452" class="stm run hide_run">                        <span class="nam">gen</span><span class="op">.</span><span class="nam">parseLine</span><span class="op">(</span><span class="nam">sCode</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t453" class="pln">                <span class="key">else</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t454" class="pln">                    <span class="com"># Deal with an ordinary code block.</span><span class="strut">&nbsp;</span></p>
+<p id="t455" class="stm run hide_run">                    <span class="nam">l</span> <span class="op">=</span> <span class="nam">fIn</span><span class="op">.</span><span class="nam">readline</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t456" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t457" class="pln">                    <span class="com"># Get all the lines in the spec</span><span class="strut">&nbsp;</span></p>
+<p id="t458" class="stm run hide_run">                    <span class="key">while</span> <span class="nam">l</span> <span class="key">and</span> <span class="key">not</span> <span class="nam">self</span><span class="op">.</span><span class="nam">isEndSpecLine</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t459" class="stm par run hide_run"><span class="annotate short">459&#x202F;&#x219B;&#x202F;460</span><span class="annotate long">line 459 didn't jump to line 460, because the condition on line 459 was never true</span>                        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">isBeginSpecLine</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t460" class="stm mis">                            <span class="key">raise</span> <span class="nam">CogError</span><span class="op">(</span><span class="str">"Unexpected '%s'"</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sBeginSpec</span><span class="op">,</span><span class="strut">&nbsp;</span></p>
+<p id="t461" class="pln">                                <span class="nam">file</span><span class="op">=</span><span class="nam">sFileIn</span><span class="op">,</span> <span class="nam">line</span><span class="op">=</span><span class="nam">fIn</span><span class="op">.</span><span class="nam">linenumber</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t462" class="stm par run hide_run"><span class="annotate short">462&#x202F;&#x219B;&#x202F;463</span><span class="annotate long">line 462 didn't jump to line 463, because the condition on line 462 was never true</span>                        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">isEndOutputLine</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t463" class="stm mis">                            <span class="key">raise</span> <span class="nam">CogError</span><span class="op">(</span><span class="str">"Unexpected '%s'"</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sEndOutput</span><span class="op">,</span><span class="strut">&nbsp;</span></p>
+<p id="t464" class="pln">                                <span class="nam">file</span><span class="op">=</span><span class="nam">sFileIn</span><span class="op">,</span> <span class="nam">line</span><span class="op">=</span><span class="nam">fIn</span><span class="op">.</span><span class="nam">linenumber</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t465" class="stm par run hide_run"><span class="annotate short">465&#x202F;&#x219B;&#x202F;467</span><span class="annotate long">line 465 didn't jump to line 467, because the condition on line 465 was never false</span>                        <span class="key">if</span> <span class="key">not</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">bDeleteCode</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t466" class="stm run hide_run">                            <span class="nam">fOut</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t467" class="stm run hide_run">                        <span class="nam">gen</span><span class="op">.</span><span class="nam">parseLine</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t468" class="stm run hide_run">                        <span class="nam">l</span> <span class="op">=</span> <span class="nam">fIn</span><span class="op">.</span><span class="nam">readline</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t469" class="stm par run hide_run"><span class="annotate short">469&#x202F;&#x219B;&#x202F;470</span><span class="annotate long">line 469 didn't jump to line 470, because the condition on line 469 was never true</span>                    <span class="key">if</span> <span class="key">not</span> <span class="nam">l</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t470" class="stm mis">                        <span class="key">raise</span> <span class="nam">CogError</span><span class="op">(</span><span class="strut">&nbsp;</span></p>
+<p id="t471" class="pln">                            <span class="str">"Cog block begun but never ended."</span><span class="op">,</span><span class="strut">&nbsp;</span></p>
+<p id="t472" class="pln">                            <span class="nam">file</span><span class="op">=</span><span class="nam">sFileIn</span><span class="op">,</span> <span class="nam">line</span><span class="op">=</span><span class="nam">firstLineNum</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t473" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t474" class="stm par run hide_run"><span class="annotate short">474&#x202F;&#x219B;&#x202F;476</span><span class="annotate long">line 474 didn't jump to line 476, because the condition on line 474 was never false</span>                    <span class="key">if</span> <span class="key">not</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">bDeleteCode</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t475" class="stm run hide_run">                        <span class="nam">fOut</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t476" class="stm run hide_run">                    <span class="nam">gen</span><span class="op">.</span><span class="nam">parseMarker</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
 <p id="t477" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t478" class="pln">                <span class="com"># Eat all the lines in the output section.  While reading past</span><span class="strut">&nbsp;</span></p>
-<p id="t479" class="pln">                <span class="com"># them, compute the md5 hash of the old output.</span><span class="strut">&nbsp;</span></p>
-<p id="t480" class="stm run hide_run">                <span class="nam">previous</span> <span class="op">=</span> <span class="str">""</span><span class="strut">&nbsp;</span></p>
-<p id="t481" class="stm run hide_run">                <span class="nam">hasher</span> <span class="op">=</span> <span class="nam">hashlib</span><span class="op">.</span><span class="nam">md5</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t482" class="stm run hide_run">                <span class="key">while</span> <span class="nam">l</span> <span class="key">and</span> <span class="key">not</span> <span class="nam">self</span><span class="op">.</span><span class="nam">isEndOutputLine</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t483" class="stm par run hide_run"><span class="annotate short">483&#x202F;&#x219B;&#x202F;484</span><span class="annotate long">line 483 didn't jump to line 484, because the condition on line 483 was never true</span>                    <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">isBeginSpecLine</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t484" class="stm mis">                        <span class="key">raise</span> <span class="nam">CogError</span><span class="op">(</span><span class="str">"Unexpected '%s'"</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sBeginSpec</span><span class="op">,</span><span class="strut">&nbsp;</span></p>
-<p id="t485" class="pln">                            <span class="nam">file</span><span class="op">=</span><span class="nam">sFileIn</span><span class="op">,</span> <span class="nam">line</span><span class="op">=</span><span class="nam">fIn</span><span class="op">.</span><span class="nam">linenumber</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t486" class="stm par run hide_run"><span class="annotate short">486&#x202F;&#x219B;&#x202F;487</span><span class="annotate long">line 486 didn't jump to line 487, because the condition on line 486 was never true</span>                    <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">isEndSpecLine</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t487" class="stm mis">                        <span class="key">raise</span> <span class="nam">CogError</span><span class="op">(</span><span class="str">"Unexpected '%s'"</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sEndSpec</span><span class="op">,</span><span class="strut">&nbsp;</span></p>
-<p id="t488" class="pln">                            <span class="nam">file</span><span class="op">=</span><span class="nam">sFileIn</span><span class="op">,</span> <span class="nam">line</span><span class="op">=</span><span class="nam">fIn</span><span class="op">.</span><span class="nam">linenumber</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t489" class="stm run hide_run">                    <span class="nam">previous</span> <span class="op">+=</span> <span class="nam">l</span><span class="strut">&nbsp;</span></p>
-<p id="t490" class="stm run hide_run">                    <span class="nam">hasher</span><span class="op">.</span><span class="nam">update</span><span class="op">(</span><span class="nam">to_bytes</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t491" class="stm run hide_run">                    <span class="nam">l</span> <span class="op">=</span> <span class="nam">fIn</span><span class="op">.</span><span class="nam">readline</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t492" class="stm run hide_run">                <span class="nam">curHash</span> <span class="op">=</span> <span class="nam">hasher</span><span class="op">.</span><span class="nam">hexdigest</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t493" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t494" class="stm par run hide_run"><span class="annotate short">494&#x202F;&#x219B;&#x202F;496</span><span class="annotate long">line 494 didn't jump to line 496, because the condition on line 494 was never true</span>                <span class="key">if</span> <span class="key">not</span> <span class="nam">l</span> <span class="key">and</span> <span class="key">not</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">bEofCanBeEnd</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t495" class="pln">                    <span class="com"># We reached end of file before we found the end output line.</span><span class="strut">&nbsp;</span></p>
-<p id="t496" class="stm mis">                    <span class="key">raise</span> <span class="nam">CogError</span><span class="op">(</span><span class="str">"Missing '%s' before end of file."</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sEndOutput</span><span class="op">,</span><span class="strut">&nbsp;</span></p>
-<p id="t497" class="pln">                        <span class="nam">file</span><span class="op">=</span><span class="nam">sFileIn</span><span class="op">,</span> <span class="nam">line</span><span class="op">=</span><span class="nam">fIn</span><span class="op">.</span><span class="nam">linenumber</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t498" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t499" class="pln">                <span class="com"># Make the previous output available to the current code</span><span class="strut">&nbsp;</span></p>
-<p id="t500" class="stm run hide_run">                <span class="nam">self</span><span class="op">.</span><span class="nam">cogmodule</span><span class="op">.</span><span class="nam">previous</span> <span class="op">=</span> <span class="nam">previous</span><span class="strut">&nbsp;</span></p>
-<p id="t501" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t502" class="pln">                <span class="com"># Write the output of the spec to be the new output if we're</span><span class="strut">&nbsp;</span></p>
-<p id="t503" class="pln">                <span class="com"># supposed to generate code.</span><span class="strut">&nbsp;</span></p>
-<p id="t504" class="stm run hide_run">                <span class="nam">hasher</span> <span class="op">=</span> <span class="nam">hashlib</span><span class="op">.</span><span class="nam">md5</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t505" class="stm par run hide_run"><span class="annotate short">505&#x202F;&#x219B;&#x202F;511</span><span class="annotate long">line 505 didn't jump to line 511, because the condition on line 505 was never false</span>                <span class="key">if</span> <span class="key">not</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">bNoGenerate</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t506" class="stm run hide_run">                    <span class="nam">sFile</span> <span class="op">=</span> <span class="str">"%s+%d"</span> <span class="op">%</span> <span class="op">(</span><span class="nam">sFileIn</span><span class="op">,</span> <span class="nam">firstLineNum</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t507" class="stm run hide_run">                    <span class="nam">sGen</span> <span class="op">=</span> <span class="nam">gen</span><span class="op">.</span><span class="nam">evaluate</span><span class="op">(</span><span class="nam">cog</span><span class="op">=</span><span class="nam">self</span><span class="op">,</span> <span class="nam">globals</span><span class="op">=</span><span class="nam">globals</span><span class="op">,</span> <span class="nam">fname</span><span class="op">=</span><span class="nam">sFile</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t508" class="stm run hide_run">                    <span class="nam">sGen</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">suffixLines</span><span class="op">(</span><span class="nam">sGen</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t509" class="stm run hide_run">                    <span class="nam">hasher</span><span class="op">.</span><span class="nam">update</span><span class="op">(</span><span class="nam">to_bytes</span><span class="op">(</span><span class="nam">sGen</span><span class="op">)</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t510" class="stm run hide_run">                    <span class="nam">fOut</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="nam">sGen</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t511" class="stm run hide_run">                <span class="nam">newHash</span> <span class="op">=</span> <span class="nam">hasher</span><span class="op">.</span><span class="nam">hexdigest</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t512" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t513" class="stm run hide_run">                <span class="nam">bSawCog</span> <span class="op">=</span> <span class="nam">True</span><span class="strut">&nbsp;</span></p>
+<p id="t478" class="stm run hide_run">                <span class="nam">l</span> <span class="op">=</span> <span class="nam">fIn</span><span class="op">.</span><span class="nam">readline</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t479" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t480" class="pln">                <span class="com"># Eat all the lines in the output section.  While reading past</span><span class="strut">&nbsp;</span></p>
+<p id="t481" class="pln">                <span class="com"># them, compute the md5 hash of the old output.</span><span class="strut">&nbsp;</span></p>
+<p id="t482" class="stm run hide_run">                <span class="nam">previous</span> <span class="op">=</span> <span class="str">""</span><span class="strut">&nbsp;</span></p>
+<p id="t483" class="stm run hide_run">                <span class="nam">hasher</span> <span class="op">=</span> <span class="nam">hashlib</span><span class="op">.</span><span class="nam">md5</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t484" class="stm run hide_run">                <span class="key">while</span> <span class="nam">l</span> <span class="key">and</span> <span class="key">not</span> <span class="nam">self</span><span class="op">.</span><span class="nam">isEndOutputLine</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t485" class="stm par run hide_run"><span class="annotate short">485&#x202F;&#x219B;&#x202F;486</span><span class="annotate long">line 485 didn't jump to line 486, because the condition on line 485 was never true</span>                    <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">isBeginSpecLine</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t486" class="stm mis">                        <span class="key">raise</span> <span class="nam">CogError</span><span class="op">(</span><span class="str">"Unexpected '%s'"</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sBeginSpec</span><span class="op">,</span><span class="strut">&nbsp;</span></p>
+<p id="t487" class="pln">                            <span class="nam">file</span><span class="op">=</span><span class="nam">sFileIn</span><span class="op">,</span> <span class="nam">line</span><span class="op">=</span><span class="nam">fIn</span><span class="op">.</span><span class="nam">linenumber</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t488" class="stm par run hide_run"><span class="annotate short">488&#x202F;&#x219B;&#x202F;489</span><span class="annotate long">line 488 didn't jump to line 489, because the condition on line 488 was never true</span>                    <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">isEndSpecLine</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t489" class="stm mis">                        <span class="key">raise</span> <span class="nam">CogError</span><span class="op">(</span><span class="str">"Unexpected '%s'"</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sEndSpec</span><span class="op">,</span><span class="strut">&nbsp;</span></p>
+<p id="t490" class="pln">                            <span class="nam">file</span><span class="op">=</span><span class="nam">sFileIn</span><span class="op">,</span> <span class="nam">line</span><span class="op">=</span><span class="nam">fIn</span><span class="op">.</span><span class="nam">linenumber</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t491" class="stm run hide_run">                    <span class="nam">previous</span> <span class="op">+=</span> <span class="nam">l</span><span class="strut">&nbsp;</span></p>
+<p id="t492" class="stm run hide_run">                    <span class="nam">hasher</span><span class="op">.</span><span class="nam">update</span><span class="op">(</span><span class="nam">to_bytes</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t493" class="stm run hide_run">                    <span class="nam">l</span> <span class="op">=</span> <span class="nam">fIn</span><span class="op">.</span><span class="nam">readline</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t494" class="stm run hide_run">                <span class="nam">curHash</span> <span class="op">=</span> <span class="nam">hasher</span><span class="op">.</span><span class="nam">hexdigest</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t495" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t496" class="stm par run hide_run"><span class="annotate short">496&#x202F;&#x219B;&#x202F;498</span><span class="annotate long">line 496 didn't jump to line 498, because the condition on line 496 was never true</span>                <span class="key">if</span> <span class="key">not</span> <span class="nam">l</span> <span class="key">and</span> <span class="key">not</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">bEofCanBeEnd</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t497" class="pln">                    <span class="com"># We reached end of file before we found the end output line.</span><span class="strut">&nbsp;</span></p>
+<p id="t498" class="stm mis">                    <span class="key">raise</span> <span class="nam">CogError</span><span class="op">(</span><span class="str">"Missing '%s' before end of file."</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sEndOutput</span><span class="op">,</span><span class="strut">&nbsp;</span></p>
+<p id="t499" class="pln">                        <span class="nam">file</span><span class="op">=</span><span class="nam">sFileIn</span><span class="op">,</span> <span class="nam">line</span><span class="op">=</span><span class="nam">fIn</span><span class="op">.</span><span class="nam">linenumber</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t500" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t501" class="pln">                <span class="com"># Make the previous output available to the current code</span><span class="strut">&nbsp;</span></p>
+<p id="t502" class="stm run hide_run">                <span class="nam">self</span><span class="op">.</span><span class="nam">cogmodule</span><span class="op">.</span><span class="nam">previous</span> <span class="op">=</span> <span class="nam">previous</span><span class="strut">&nbsp;</span></p>
+<p id="t503" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t504" class="pln">                <span class="com"># Write the output of the spec to be the new output if we're</span><span class="strut">&nbsp;</span></p>
+<p id="t505" class="pln">                <span class="com"># supposed to generate code.</span><span class="strut">&nbsp;</span></p>
+<p id="t506" class="stm run hide_run">                <span class="nam">hasher</span> <span class="op">=</span> <span class="nam">hashlib</span><span class="op">.</span><span class="nam">md5</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t507" class="stm par run hide_run"><span class="annotate short">507&#x202F;&#x219B;&#x202F;513</span><span class="annotate long">line 507 didn't jump to line 513, because the condition on line 507 was never false</span>                <span class="key">if</span> <span class="key">not</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">bNoGenerate</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t508" class="stm run hide_run">                    <span class="nam">sFile</span> <span class="op">=</span> <span class="str">"%s+%d"</span> <span class="op">%</span> <span class="op">(</span><span class="nam">sFileIn</span><span class="op">,</span> <span class="nam">firstLineNum</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t509" class="stm run hide_run">                    <span class="nam">sGen</span> <span class="op">=</span> <span class="nam">gen</span><span class="op">.</span><span class="nam">evaluate</span><span class="op">(</span><span class="nam">cog</span><span class="op">=</span><span class="nam">self</span><span class="op">,</span> <span class="nam">globals</span><span class="op">=</span><span class="nam">globals</span><span class="op">,</span> <span class="nam">fname</span><span class="op">=</span><span class="nam">sFile</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t510" class="stm run hide_run">                    <span class="nam">sGen</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">suffixLines</span><span class="op">(</span><span class="nam">sGen</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t511" class="stm run hide_run">                    <span class="nam">hasher</span><span class="op">.</span><span class="nam">update</span><span class="op">(</span><span class="nam">to_bytes</span><span class="op">(</span><span class="nam">sGen</span><span class="op">)</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t512" class="stm run hide_run">                    <span class="nam">fOut</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="nam">sGen</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t513" class="stm run hide_run">                <span class="nam">newHash</span> <span class="op">=</span> <span class="nam">hasher</span><span class="op">.</span><span class="nam">hexdigest</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
 <p id="t514" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t515" class="pln">                <span class="com"># Write the ending output line</span><span class="strut">&nbsp;</span></p>
-<p id="t516" class="stm run hide_run">                <span class="nam">hashMatch</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">reEndOutput</span><span class="op">.</span><span class="nam">search</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t517" class="stm par run hide_run"><span class="annotate short">517&#x202F;&#x219B;&#x202F;518</span><span class="annotate long">line 517 didn't jump to line 518, because the condition on line 517 was never true</span>                <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">bHashOutput</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t518" class="stm mis">                    <span class="key">if</span> <span class="nam">hashMatch</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t519" class="stm mis">                        <span class="nam">oldHash</span> <span class="op">=</span> <span class="nam">hashMatch</span><span class="op">.</span><span class="nam">groupdict</span><span class="op">(</span><span class="op">)</span><span class="op">[</span><span class="str">'hash'</span><span class="op">]</span><span class="strut">&nbsp;</span></p>
-<p id="t520" class="stm mis">                        <span class="key">if</span> <span class="nam">oldHash</span> <span class="op">!=</span> <span class="nam">curHash</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t521" class="stm mis">                            <span class="key">raise</span> <span class="nam">CogError</span><span class="op">(</span><span class="str">"Output has been edited! Delete old checksum to unprotect."</span><span class="op">,</span><span class="strut">&nbsp;</span></p>
-<p id="t522" class="pln">                                <span class="nam">file</span><span class="op">=</span><span class="nam">sFileIn</span><span class="op">,</span> <span class="nam">line</span><span class="op">=</span><span class="nam">fIn</span><span class="op">.</span><span class="nam">linenumber</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t523" class="pln">                        <span class="com"># Create a new end line with the correct hash.</span><span class="strut">&nbsp;</span></p>
-<p id="t524" class="stm mis">                        <span class="nam">endpieces</span> <span class="op">=</span> <span class="nam">l</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="nam">hashMatch</span><span class="op">.</span><span class="nam">group</span><span class="op">(</span><span class="num">0</span><span class="op">)</span><span class="op">,</span> <span class="num">1</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t525" class="pln">                    <span class="key">else</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t526" class="pln">                        <span class="com"># There was no old hash, but we want a new hash.</span><span class="strut">&nbsp;</span></p>
-<p id="t527" class="stm mis">                        <span class="nam">endpieces</span> <span class="op">=</span> <span class="nam">l</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sEndOutput</span><span class="op">,</span> <span class="num">1</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t528" class="stm mis">                    <span class="nam">l</span> <span class="op">=</span> <span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sEndFormat</span> <span class="op">%</span> <span class="nam">newHash</span><span class="op">)</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">endpieces</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t529" class="pln">                <span class="key">else</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t530" class="pln">                    <span class="com"># We don't want hashes output, so if there was one, get rid of</span><span class="strut">&nbsp;</span></p>
-<p id="t531" class="pln">                    <span class="com"># it.</span><span class="strut">&nbsp;</span></p>
-<p id="t532" class="stm par run hide_run"><span class="annotate short">532&#x202F;&#x219B;&#x202F;533</span><span class="annotate long">line 532 didn't jump to line 533, because the condition on line 532 was never true</span>                    <span class="key">if</span> <span class="nam">hashMatch</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t533" class="stm mis">                        <span class="nam">l</span> <span class="op">=</span> <span class="nam">l</span><span class="op">.</span><span class="nam">replace</span><span class="op">(</span><span class="nam">hashMatch</span><span class="op">.</span><span class="nam">groupdict</span><span class="op">(</span><span class="op">)</span><span class="op">[</span><span class="str">'hashsect'</span><span class="op">]</span><span class="op">,</span> <span class="str">''</span><span class="op">,</span> <span class="num">1</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t534" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t535" class="stm par run hide_run"><span class="annotate short">535&#x202F;&#x219B;&#x202F;537</span><span class="annotate long">line 535 didn't jump to line 537, because the condition on line 535 was never false</span>                <span class="key">if</span> <span class="key">not</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">bDeleteCode</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t536" class="stm run hide_run">                    <span class="nam">fOut</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t537" class="stm run hide_run">                <span class="nam">l</span> <span class="op">=</span> <span class="nam">fIn</span><span class="op">.</span><span class="nam">readline</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t538" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t539" class="stm par run hide_run"><span class="annotate short">539&#x202F;&#x219B;&#x202F;540</span><span class="annotate long">line 539 didn't jump to line 540, because the condition on line 539 was never true</span>            <span class="key">if</span> <span class="key">not</span> <span class="nam">bSawCog</span> <span class="key">and</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">bWarnEmpty</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t540" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">showWarning</span><span class="op">(</span><span class="str">"no cog code found in %s"</span> <span class="op">%</span> <span class="nam">sFileIn</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t541" class="pln">        <span class="key">finally</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t542" class="stm par run hide_run"><span class="annotate short">542&#x202F;&#x219B;&#x202F;543</span><span class="annotate long">line 542 didn't jump to line 543, because the condition on line 542 was never true</span>            <span class="key">if</span> <span class="nam">fInToClose</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t543" class="stm mis">                <span class="nam">fInToClose</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t544" class="stm par run hide_run"><span class="annotate short">544&#x202F;&#x219B;&#x202F;545</span><span class="annotate long">line 544 didn't jump to line 545, because the condition on line 544 was never true</span>            <span class="key">if</span> <span class="nam">fOutToClose</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t545" class="stm mis">                <span class="nam">fOutToClose</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t546" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t547" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t548" class="pln">    <span class="com"># A regex for non-empty lines, used by suffixLines.</span><span class="strut">&nbsp;</span></p>
-<p id="t549" class="stm run hide_run">    <span class="nam">reNonEmptyLines</span> <span class="op">=</span> <span class="nam">re</span><span class="op">.</span><span class="nam">compile</span><span class="op">(</span><span class="str">"^\s*\S+.*$"</span><span class="op">,</span> <span class="nam">re</span><span class="op">.</span><span class="nam">MULTILINE</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t550" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t551" class="stm run hide_run">    <span class="key">def</span> <span class="nam">suffixLines</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">text</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t552" class="pln">        <span class="str">""" Add suffixes to the lines in text, if our options desire it.</span><span class="strut">&nbsp;</span></p>
-<p id="t553" class="pln"><span class="str">            text is many lines, as a single string.</span><span class="strut">&nbsp;</span></p>
-<p id="t554" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
-<p id="t555" class="stm par run hide_run"><span class="annotate short">555&#x202F;&#x219B;&#x202F;557</span><span class="annotate long">line 555 didn't jump to line 557, because the condition on line 555 was never true</span>        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sSuffix</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t556" class="pln">            <span class="com"># Find all non-blank lines, and add the suffix to the end.</span><span class="strut">&nbsp;</span></p>
-<p id="t557" class="stm mis">            <span class="nam">repl</span> <span class="op">=</span> <span class="str">r"\g&lt;0>"</span> <span class="op">+</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sSuffix</span><span class="op">.</span><span class="nam">replace</span><span class="op">(</span><span class="str">'\\'</span><span class="op">,</span> <span class="str">'\\\\'</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t558" class="stm mis">            <span class="nam">text</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">reNonEmptyLines</span><span class="op">.</span><span class="nam">sub</span><span class="op">(</span><span class="nam">repl</span><span class="op">,</span> <span class="nam">text</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t559" class="stm run hide_run">        <span class="key">return</span> <span class="nam">text</span><span class="strut">&nbsp;</span></p>
-<p id="t560" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t561" class="stm run hide_run">    <span class="key">def</span> <span class="nam">processString</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">sInput</span><span class="op">,</span> <span class="nam">fname</span><span class="op">=</span><span class="nam">None</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t562" class="pln">        <span class="str">""" Process sInput as the text to cog.</span><span class="strut">&nbsp;</span></p>
-<p id="t563" class="pln"><span class="str">            Return the cogged output as a string.</span><span class="strut">&nbsp;</span></p>
-<p id="t564" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
-<p id="t565" class="stm run hide_run">        <span class="nam">fOld</span> <span class="op">=</span> <span class="nam">StringIO</span><span class="op">(</span><span class="nam">sInput</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t566" class="stm run hide_run">        <span class="nam">fNew</span> <span class="op">=</span> <span class="nam">StringIO</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t567" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">processFile</span><span class="op">(</span><span class="nam">fOld</span><span class="op">,</span> <span class="nam">fNew</span><span class="op">,</span> <span class="nam">fname</span><span class="op">=</span><span class="nam">fname</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t568" class="stm run hide_run">        <span class="key">return</span> <span class="nam">fNew</span><span class="op">.</span><span class="nam">getvalue</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t569" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t570" class="stm run hide_run">    <span class="key">def</span> <span class="nam">replaceFile</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">sOldPath</span><span class="op">,</span> <span class="nam">sNewText</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t571" class="pln">        <span class="str">""" Replace file sOldPath with the contents sNewText</span><span class="strut">&nbsp;</span></p>
-<p id="t572" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
-<p id="t573" class="stm mis">        <span class="key">if</span> <span class="key">not</span> <span class="nam">os</span><span class="op">.</span><span class="nam">access</span><span class="op">(</span><span class="nam">sOldPath</span><span class="op">,</span> <span class="nam">os</span><span class="op">.</span><span class="nam">W_OK</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t574" class="pln">            <span class="com"># Need to ensure we can write.</span><span class="strut">&nbsp;</span></p>
-<p id="t575" class="stm mis">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sMakeWritableCmd</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t576" class="pln">                <span class="com"># Use an external command to make the file writable.</span><span class="strut">&nbsp;</span></p>
-<p id="t577" class="stm mis">                <span class="nam">cmd</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sMakeWritableCmd</span><span class="op">.</span><span class="nam">replace</span><span class="op">(</span><span class="str">'%s'</span><span class="op">,</span> <span class="nam">sOldPath</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t578" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">stdout</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="nam">os</span><span class="op">.</span><span class="nam">popen</span><span class="op">(</span><span class="nam">cmd</span><span class="op">)</span><span class="op">.</span><span class="nam">read</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t579" class="stm mis">                <span class="key">if</span> <span class="key">not</span> <span class="nam">os</span><span class="op">.</span><span class="nam">access</span><span class="op">(</span><span class="nam">sOldPath</span><span class="op">,</span> <span class="nam">os</span><span class="op">.</span><span class="nam">W_OK</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t580" class="stm mis">                    <span class="key">raise</span> <span class="nam">CogError</span><span class="op">(</span><span class="str">"Couldn't make %s writable"</span> <span class="op">%</span> <span class="nam">sOldPath</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t581" class="pln">            <span class="key">else</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t582" class="pln">                <span class="com"># Can't write!</span><span class="strut">&nbsp;</span></p>
-<p id="t583" class="stm mis">                <span class="key">raise</span> <span class="nam">CogError</span><span class="op">(</span><span class="str">"Can't overwrite %s"</span> <span class="op">%</span> <span class="nam">sOldPath</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t584" class="stm mis">        <span class="nam">f</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">openOutputFile</span><span class="op">(</span><span class="nam">sOldPath</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t585" class="stm mis">        <span class="nam">f</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="nam">sNewText</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t586" class="stm mis">        <span class="nam">f</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t587" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t588" class="stm run hide_run">    <span class="key">def</span> <span class="nam">saveIncludePath</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t589" class="stm mis">        <span class="nam">self</span><span class="op">.</span><span class="nam">savedInclude</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">includePath</span><span class="op">[</span><span class="op">:</span><span class="op">]</span><span class="strut">&nbsp;</span></p>
-<p id="t590" class="stm mis">        <span class="nam">self</span><span class="op">.</span><span class="nam">savedSysPath</span> <span class="op">=</span> <span class="nam">sys</span><span class="op">.</span><span class="nam">path</span><span class="op">[</span><span class="op">:</span><span class="op">]</span><span class="strut">&nbsp;</span></p>
-<p id="t591" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t592" class="stm run hide_run">    <span class="key">def</span> <span class="nam">restoreIncludePath</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t593" class="stm mis">        <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">includePath</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">savedInclude</span><span class="strut">&nbsp;</span></p>
-<p id="t594" class="stm mis">        <span class="nam">self</span><span class="op">.</span><span class="nam">cogmodule</span><span class="op">.</span><span class="nam">path</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">includePath</span><span class="strut">&nbsp;</span></p>
-<p id="t595" class="stm mis">        <span class="nam">sys</span><span class="op">.</span><span class="nam">path</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">savedSysPath</span><span class="strut">&nbsp;</span></p>
-<p id="t596" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t597" class="stm run hide_run">    <span class="key">def</span> <span class="nam">addToIncludePath</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">includePath</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t598" class="stm mis">        <span class="nam">self</span><span class="op">.</span><span class="nam">cogmodule</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="nam">includePath</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t599" class="stm mis">        <span class="nam">sys</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="nam">includePath</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t600" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t601" class="stm run hide_run">    <span class="key">def</span> <span class="nam">processOneFile</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">sFile</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t602" class="pln">        <span class="str">""" Process one filename through cog.</span><span class="strut">&nbsp;</span></p>
-<p id="t603" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
-<p id="t604" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t605" class="stm mis">        <span class="nam">self</span><span class="op">.</span><span class="nam">saveIncludePath</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t606" class="stm mis">        <span class="nam">bNeedNewline</span> <span class="op">=</span> <span class="nam">False</span><span class="strut">&nbsp;</span></p>
-<p id="t607" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t608" class="stm mis">        <span class="key">try</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t609" class="stm mis">            <span class="nam">self</span><span class="op">.</span><span class="nam">addToIncludePath</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">includePath</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t610" class="pln">            <span class="com"># Since we know where the input file came from,</span><span class="strut">&nbsp;</span></p>
-<p id="t611" class="pln">            <span class="com"># push its directory onto the include path.</span><span class="strut">&nbsp;</span></p>
-<p id="t612" class="stm mis">            <span class="nam">self</span><span class="op">.</span><span class="nam">addToIncludePath</span><span class="op">(</span><span class="op">[</span><span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">dirname</span><span class="op">(</span><span class="nam">sFile</span><span class="op">)</span><span class="op">]</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t613" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t614" class="pln">            <span class="com"># How we process the file depends on where the output is going.</span><span class="strut">&nbsp;</span></p>
-<p id="t615" class="stm mis">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sOutputName</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t616" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">processFile</span><span class="op">(</span><span class="nam">sFile</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sOutputName</span><span class="op">,</span> <span class="nam">sFile</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t617" class="stm mis">            <span class="key">elif</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">bReplace</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t618" class="pln">                <span class="com"># We want to replace the cog file with the output,</span><span class="strut">&nbsp;</span></p>
-<p id="t619" class="pln">                <span class="com"># but only if they differ.</span><span class="strut">&nbsp;</span></p>
-<p id="t620" class="stm mis">                <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">verbosity</span> <span class="op">>=</span> <span class="num">2</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t621" class="stm mis">                    <span class="nam">self</span><span class="op">.</span><span class="nam">prout</span><span class="op">(</span><span class="str">"Cogging %s"</span> <span class="op">%</span> <span class="nam">sFile</span><span class="op">,</span> <span class="nam">end</span><span class="op">=</span><span class="str">""</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t622" class="stm mis">                    <span class="nam">bNeedNewline</span> <span class="op">=</span> <span class="nam">True</span><span class="strut">&nbsp;</span></p>
-<p id="t623" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t624" class="stm mis">                <span class="key">try</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t625" class="stm mis">                    <span class="nam">fOldFile</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">openInputFile</span><span class="op">(</span><span class="nam">sFile</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t626" class="stm mis">                    <span class="nam">sOldText</span> <span class="op">=</span> <span class="nam">fOldFile</span><span class="op">.</span><span class="nam">read</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t627" class="stm mis">                    <span class="nam">fOldFile</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t628" class="stm mis">                    <span class="nam">sNewText</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">processString</span><span class="op">(</span><span class="nam">sOldText</span><span class="op">,</span> <span class="nam">fname</span><span class="op">=</span><span class="nam">sFile</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t629" class="stm mis">                    <span class="key">if</span> <span class="nam">sOldText</span> <span class="op">!=</span> <span class="nam">sNewText</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t630" class="stm mis">                        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">verbosity</span> <span class="op">>=</span> <span class="num">1</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t631" class="stm mis">                            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">verbosity</span> <span class="op">&lt;</span> <span class="num">2</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t632" class="stm mis">                                <span class="nam">self</span><span class="op">.</span><span class="nam">prout</span><span class="op">(</span><span class="str">"Cogging %s"</span> <span class="op">%</span> <span class="nam">sFile</span><span class="op">,</span> <span class="nam">end</span><span class="op">=</span><span class="str">""</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t633" class="stm mis">                            <span class="nam">self</span><span class="op">.</span><span class="nam">prout</span><span class="op">(</span><span class="str">"  (changed)"</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t634" class="stm mis">                            <span class="nam">bNeedNewline</span> <span class="op">=</span> <span class="nam">False</span><span class="strut">&nbsp;</span></p>
-<p id="t635" class="stm mis">                        <span class="nam">self</span><span class="op">.</span><span class="nam">replaceFile</span><span class="op">(</span><span class="nam">sFile</span><span class="op">,</span> <span class="nam">sNewText</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t636" class="pln">                <span class="key">finally</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t637" class="pln">                    <span class="com"># The try-finally block is so we can print a partial line</span><span class="strut">&nbsp;</span></p>
-<p id="t638" class="pln">                    <span class="com"># with the name of the file, and print (changed) on the</span><span class="strut">&nbsp;</span></p>
-<p id="t639" class="pln">                    <span class="com"># same line, but also make sure to break the line before</span><span class="strut">&nbsp;</span></p>
-<p id="t640" class="pln">                    <span class="com"># any traceback.</span><span class="strut">&nbsp;</span></p>
-<p id="t641" class="stm mis">                    <span class="key">if</span> <span class="nam">bNeedNewline</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t642" class="stm mis">                        <span class="nam">self</span><span class="op">.</span><span class="nam">prout</span><span class="op">(</span><span class="str">""</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t643" class="pln">            <span class="key">else</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t644" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">processFile</span><span class="op">(</span><span class="nam">sFile</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">stdout</span><span class="op">,</span> <span class="nam">sFile</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t645" class="pln">        <span class="key">finally</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t646" class="stm mis">            <span class="nam">self</span><span class="op">.</span><span class="nam">restoreIncludePath</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t647" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t648" class="stm run hide_run">    <span class="key">def</span> <span class="nam">processFileList</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">sFileList</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t649" class="pln">        <span class="str">""" Process the files in a file list.</span><span class="strut">&nbsp;</span></p>
-<p id="t650" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
-<p id="t651" class="stm mis">        <span class="nam">flist</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">openInputFile</span><span class="op">(</span><span class="nam">sFileList</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t652" class="stm mis">        <span class="nam">lines</span> <span class="op">=</span> <span class="nam">flist</span><span class="op">.</span><span class="nam">readlines</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t653" class="stm mis">        <span class="nam">flist</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t654" class="stm mis">        <span class="key">for</span> <span class="nam">l</span> <span class="key">in</span> <span class="nam">lines</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t655" class="pln">            <span class="com"># Use shlex to parse the line like a shell.</span><span class="strut">&nbsp;</span></p>
-<p id="t656" class="stm mis">            <span class="nam">lex</span> <span class="op">=</span> <span class="nam">shlex</span><span class="op">.</span><span class="nam">shlex</span><span class="op">(</span><span class="nam">l</span><span class="op">,</span> <span class="nam">posix</span><span class="op">=</span><span class="nam">True</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t657" class="stm mis">            <span class="nam">lex</span><span class="op">.</span><span class="nam">whitespace_split</span> <span class="op">=</span> <span class="nam">True</span><span class="strut">&nbsp;</span></p>
-<p id="t658" class="stm mis">            <span class="nam">lex</span><span class="op">.</span><span class="nam">commenters</span> <span class="op">=</span> <span class="str">'#'</span><span class="strut">&nbsp;</span></p>
-<p id="t659" class="pln">            <span class="com"># No escapes, so that backslash can be part of the path</span><span class="strut">&nbsp;</span></p>
-<p id="t660" class="stm mis">            <span class="nam">lex</span><span class="op">.</span><span class="nam">escape</span> <span class="op">=</span> <span class="str">''</span><span class="strut">&nbsp;</span></p>
-<p id="t661" class="stm mis">            <span class="nam">args</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="nam">lex</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t662" class="stm mis">            <span class="key">if</span> <span class="nam">args</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t663" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">processArguments</span><span class="op">(</span><span class="nam">args</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t664" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t665" class="stm run hide_run">    <span class="key">def</span> <span class="nam">processArguments</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">args</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t666" class="pln">        <span class="str">""" Process one command-line.</span><span class="strut">&nbsp;</span></p>
-<p id="t667" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
-<p id="t668" class="stm mis">        <span class="nam">saved_options</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="strut">&nbsp;</span></p>
-<p id="t669" class="stm mis">        <span class="nam">self</span><span class="op">.</span><span class="nam">options</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">clone</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t670" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t671" class="stm mis">        <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">parseArgs</span><span class="op">(</span><span class="nam">args</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">]</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t672" class="stm mis">        <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">validate</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t673" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t674" class="stm mis">        <span class="key">if</span> <span class="nam">args</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">==</span> <span class="str">'@'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t675" class="stm mis">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sOutputName</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t676" class="stm mis">                <span class="key">raise</span> <span class="nam">CogUsageError</span><span class="op">(</span><span class="str">"Can't use -o with @file"</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t677" class="stm mis">            <span class="nam">self</span><span class="op">.</span><span class="nam">processFileList</span><span class="op">(</span><span class="nam">args</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">]</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t678" class="pln">        <span class="key">else</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t679" class="stm mis">            <span class="nam">self</span><span class="op">.</span><span class="nam">processOneFile</span><span class="op">(</span><span class="nam">args</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t680" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t681" class="stm mis">        <span class="nam">self</span><span class="op">.</span><span class="nam">options</span> <span class="op">=</span> <span class="nam">saved_options</span><span class="strut">&nbsp;</span></p>
+<p id="t515" class="stm run hide_run">                <span class="nam">bSawCog</span> <span class="op">=</span> <span class="nam">True</span><span class="strut">&nbsp;</span></p>
+<p id="t516" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t517" class="pln">                <span class="com"># Write the ending output line</span><span class="strut">&nbsp;</span></p>
+<p id="t518" class="stm run hide_run">                <span class="nam">hashMatch</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">reEndOutput</span><span class="op">.</span><span class="nam">search</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t519" class="stm par run hide_run"><span class="annotate short">519&#x202F;&#x219B;&#x202F;520</span><span class="annotate long">line 519 didn't jump to line 520, because the condition on line 519 was never true</span>                <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">bHashOutput</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t520" class="stm mis">                    <span class="key">if</span> <span class="nam">hashMatch</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t521" class="stm mis">                        <span class="nam">oldHash</span> <span class="op">=</span> <span class="nam">hashMatch</span><span class="op">.</span><span class="nam">groupdict</span><span class="op">(</span><span class="op">)</span><span class="op">[</span><span class="str">'hash'</span><span class="op">]</span><span class="strut">&nbsp;</span></p>
+<p id="t522" class="stm mis">                        <span class="key">if</span> <span class="nam">oldHash</span> <span class="op">!=</span> <span class="nam">curHash</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t523" class="stm mis">                            <span class="key">raise</span> <span class="nam">CogError</span><span class="op">(</span><span class="str">"Output has been edited! Delete old checksum to unprotect."</span><span class="op">,</span><span class="strut">&nbsp;</span></p>
+<p id="t524" class="pln">                                <span class="nam">file</span><span class="op">=</span><span class="nam">sFileIn</span><span class="op">,</span> <span class="nam">line</span><span class="op">=</span><span class="nam">fIn</span><span class="op">.</span><span class="nam">linenumber</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t525" class="pln">                        <span class="com"># Create a new end line with the correct hash.</span><span class="strut">&nbsp;</span></p>
+<p id="t526" class="stm mis">                        <span class="nam">endpieces</span> <span class="op">=</span> <span class="nam">l</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="nam">hashMatch</span><span class="op">.</span><span class="nam">group</span><span class="op">(</span><span class="num">0</span><span class="op">)</span><span class="op">,</span> <span class="num">1</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t527" class="pln">                    <span class="key">else</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t528" class="pln">                        <span class="com"># There was no old hash, but we want a new hash.</span><span class="strut">&nbsp;</span></p>
+<p id="t529" class="stm mis">                        <span class="nam">endpieces</span> <span class="op">=</span> <span class="nam">l</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sEndOutput</span><span class="op">,</span> <span class="num">1</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t530" class="stm mis">                    <span class="nam">l</span> <span class="op">=</span> <span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sEndFormat</span> <span class="op">%</span> <span class="nam">newHash</span><span class="op">)</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">endpieces</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t531" class="pln">                <span class="key">else</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t532" class="pln">                    <span class="com"># We don't want hashes output, so if there was one, get rid of</span><span class="strut">&nbsp;</span></p>
+<p id="t533" class="pln">                    <span class="com"># it.</span><span class="strut">&nbsp;</span></p>
+<p id="t534" class="stm par run hide_run"><span class="annotate short">534&#x202F;&#x219B;&#x202F;535</span><span class="annotate long">line 534 didn't jump to line 535, because the condition on line 534 was never true</span>                    <span class="key">if</span> <span class="nam">hashMatch</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t535" class="stm mis">                        <span class="nam">l</span> <span class="op">=</span> <span class="nam">l</span><span class="op">.</span><span class="nam">replace</span><span class="op">(</span><span class="nam">hashMatch</span><span class="op">.</span><span class="nam">groupdict</span><span class="op">(</span><span class="op">)</span><span class="op">[</span><span class="str">'hashsect'</span><span class="op">]</span><span class="op">,</span> <span class="str">''</span><span class="op">,</span> <span class="num">1</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t536" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t537" class="stm par run hide_run"><span class="annotate short">537&#x202F;&#x219B;&#x202F;539</span><span class="annotate long">line 537 didn't jump to line 539, because the condition on line 537 was never false</span>                <span class="key">if</span> <span class="key">not</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">bDeleteCode</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t538" class="stm run hide_run">                    <span class="nam">fOut</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="nam">l</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t539" class="stm run hide_run">                <span class="nam">l</span> <span class="op">=</span> <span class="nam">fIn</span><span class="op">.</span><span class="nam">readline</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t540" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t541" class="stm par run hide_run"><span class="annotate short">541&#x202F;&#x219B;&#x202F;542</span><span class="annotate long">line 541 didn't jump to line 542, because the condition on line 541 was never true</span>            <span class="key">if</span> <span class="key">not</span> <span class="nam">bSawCog</span> <span class="key">and</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">bWarnEmpty</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t542" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">showWarning</span><span class="op">(</span><span class="str">"no cog code found in %s"</span> <span class="op">%</span> <span class="nam">sFileIn</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t543" class="pln">        <span class="key">finally</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t544" class="stm par run hide_run"><span class="annotate short">544&#x202F;&#x219B;&#x202F;545</span><span class="annotate long">line 544 didn't jump to line 545, because the condition on line 544 was never true</span>            <span class="key">if</span> <span class="nam">fInToClose</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t545" class="stm mis">                <span class="nam">fInToClose</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t546" class="stm par run hide_run"><span class="annotate short">546&#x202F;&#x219B;&#x202F;547</span><span class="annotate long">line 546 didn't jump to line 547, because the condition on line 546 was never true</span>            <span class="key">if</span> <span class="nam">fOutToClose</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t547" class="stm mis">                <span class="nam">fOutToClose</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t548" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t549" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t550" class="pln">    <span class="com"># A regex for non-empty lines, used by suffixLines.</span><span class="strut">&nbsp;</span></p>
+<p id="t551" class="stm run hide_run">    <span class="nam">reNonEmptyLines</span> <span class="op">=</span> <span class="nam">re</span><span class="op">.</span><span class="nam">compile</span><span class="op">(</span><span class="str">"^\s*\S+.*$"</span><span class="op">,</span> <span class="nam">re</span><span class="op">.</span><span class="nam">MULTILINE</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t552" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t553" class="stm run hide_run">    <span class="key">def</span> <span class="nam">suffixLines</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">text</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t554" class="pln">        <span class="str">""" Add suffixes to the lines in text, if our options desire it.</span><span class="strut">&nbsp;</span></p>
+<p id="t555" class="pln"><span class="str">            text is many lines, as a single string.</span><span class="strut">&nbsp;</span></p>
+<p id="t556" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
+<p id="t557" class="stm par run hide_run"><span class="annotate short">557&#x202F;&#x219B;&#x202F;559</span><span class="annotate long">line 557 didn't jump to line 559, because the condition on line 557 was never true</span>        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sSuffix</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t558" class="pln">            <span class="com"># Find all non-blank lines, and add the suffix to the end.</span><span class="strut">&nbsp;</span></p>
+<p id="t559" class="stm mis">            <span class="nam">repl</span> <span class="op">=</span> <span class="str">r"\g&lt;0>"</span> <span class="op">+</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sSuffix</span><span class="op">.</span><span class="nam">replace</span><span class="op">(</span><span class="str">'\\'</span><span class="op">,</span> <span class="str">'\\\\'</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t560" class="stm mis">            <span class="nam">text</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">reNonEmptyLines</span><span class="op">.</span><span class="nam">sub</span><span class="op">(</span><span class="nam">repl</span><span class="op">,</span> <span class="nam">text</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t561" class="stm run hide_run">        <span class="key">return</span> <span class="nam">text</span><span class="strut">&nbsp;</span></p>
+<p id="t562" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t563" class="stm run hide_run">    <span class="key">def</span> <span class="nam">processString</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">sInput</span><span class="op">,</span> <span class="nam">fname</span><span class="op">=</span><span class="nam">None</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t564" class="pln">        <span class="str">""" Process sInput as the text to cog.</span><span class="strut">&nbsp;</span></p>
+<p id="t565" class="pln"><span class="str">            Return the cogged output as a string.</span><span class="strut">&nbsp;</span></p>
+<p id="t566" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
+<p id="t567" class="stm run hide_run">        <span class="nam">fOld</span> <span class="op">=</span> <span class="nam">StringIO</span><span class="op">(</span><span class="nam">sInput</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t568" class="stm run hide_run">        <span class="nam">fNew</span> <span class="op">=</span> <span class="nam">StringIO</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t569" class="stm run hide_run">        <span class="nam">self</span><span class="op">.</span><span class="nam">processFile</span><span class="op">(</span><span class="nam">fOld</span><span class="op">,</span> <span class="nam">fNew</span><span class="op">,</span> <span class="nam">fname</span><span class="op">=</span><span class="nam">fname</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t570" class="stm run hide_run">        <span class="key">return</span> <span class="nam">fNew</span><span class="op">.</span><span class="nam">getvalue</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t571" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t572" class="stm run hide_run">    <span class="key">def</span> <span class="nam">replaceFile</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">sOldPath</span><span class="op">,</span> <span class="nam">sNewText</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t573" class="pln">        <span class="str">""" Replace file sOldPath with the contents sNewText</span><span class="strut">&nbsp;</span></p>
+<p id="t574" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
+<p id="t575" class="stm mis">        <span class="key">if</span> <span class="key">not</span> <span class="nam">os</span><span class="op">.</span><span class="nam">access</span><span class="op">(</span><span class="nam">sOldPath</span><span class="op">,</span> <span class="nam">os</span><span class="op">.</span><span class="nam">W_OK</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t576" class="pln">            <span class="com"># Need to ensure we can write.</span><span class="strut">&nbsp;</span></p>
+<p id="t577" class="stm mis">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sMakeWritableCmd</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t578" class="pln">                <span class="com"># Use an external command to make the file writable.</span><span class="strut">&nbsp;</span></p>
+<p id="t579" class="stm mis">                <span class="nam">cmd</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sMakeWritableCmd</span><span class="op">.</span><span class="nam">replace</span><span class="op">(</span><span class="str">'%s'</span><span class="op">,</span> <span class="nam">sOldPath</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t580" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">stdout</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="nam">os</span><span class="op">.</span><span class="nam">popen</span><span class="op">(</span><span class="nam">cmd</span><span class="op">)</span><span class="op">.</span><span class="nam">read</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t581" class="stm mis">                <span class="key">if</span> <span class="key">not</span> <span class="nam">os</span><span class="op">.</span><span class="nam">access</span><span class="op">(</span><span class="nam">sOldPath</span><span class="op">,</span> <span class="nam">os</span><span class="op">.</span><span class="nam">W_OK</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t582" class="stm mis">                    <span class="key">raise</span> <span class="nam">CogError</span><span class="op">(</span><span class="str">"Couldn't make %s writable"</span> <span class="op">%</span> <span class="nam">sOldPath</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t583" class="pln">            <span class="key">else</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t584" class="pln">                <span class="com"># Can't write!</span><span class="strut">&nbsp;</span></p>
+<p id="t585" class="stm mis">                <span class="key">raise</span> <span class="nam">CogError</span><span class="op">(</span><span class="str">"Can't overwrite %s"</span> <span class="op">%</span> <span class="nam">sOldPath</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t586" class="stm mis">        <span class="nam">f</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">openOutputFile</span><span class="op">(</span><span class="nam">sOldPath</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t587" class="stm mis">        <span class="nam">f</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="nam">sNewText</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t588" class="stm mis">        <span class="nam">f</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t589" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t590" class="stm run hide_run">    <span class="key">def</span> <span class="nam">saveIncludePath</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t591" class="stm mis">        <span class="nam">self</span><span class="op">.</span><span class="nam">savedInclude</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">includePath</span><span class="op">[</span><span class="op">:</span><span class="op">]</span><span class="strut">&nbsp;</span></p>
+<p id="t592" class="stm mis">        <span class="nam">self</span><span class="op">.</span><span class="nam">savedSysPath</span> <span class="op">=</span> <span class="nam">sys</span><span class="op">.</span><span class="nam">path</span><span class="op">[</span><span class="op">:</span><span class="op">]</span><span class="strut">&nbsp;</span></p>
+<p id="t593" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t594" class="stm run hide_run">    <span class="key">def</span> <span class="nam">restoreIncludePath</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t595" class="stm mis">        <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">includePath</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">savedInclude</span><span class="strut">&nbsp;</span></p>
+<p id="t596" class="stm mis">        <span class="nam">self</span><span class="op">.</span><span class="nam">cogmodule</span><span class="op">.</span><span class="nam">path</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">includePath</span><span class="strut">&nbsp;</span></p>
+<p id="t597" class="stm mis">        <span class="nam">sys</span><span class="op">.</span><span class="nam">path</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">savedSysPath</span><span class="strut">&nbsp;</span></p>
+<p id="t598" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t599" class="stm run hide_run">    <span class="key">def</span> <span class="nam">addToIncludePath</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">includePath</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t600" class="stm mis">        <span class="nam">self</span><span class="op">.</span><span class="nam">cogmodule</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="nam">includePath</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t601" class="stm mis">        <span class="nam">sys</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="nam">includePath</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t602" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t603" class="stm run hide_run">    <span class="key">def</span> <span class="nam">processOneFile</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">sFile</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t604" class="pln">        <span class="str">""" Process one filename through cog.</span><span class="strut">&nbsp;</span></p>
+<p id="t605" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
+<p id="t606" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t607" class="stm mis">        <span class="nam">self</span><span class="op">.</span><span class="nam">saveIncludePath</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t608" class="stm mis">        <span class="nam">bNeedNewline</span> <span class="op">=</span> <span class="nam">False</span><span class="strut">&nbsp;</span></p>
+<p id="t609" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t610" class="stm mis">        <span class="key">try</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t611" class="stm mis">            <span class="nam">self</span><span class="op">.</span><span class="nam">addToIncludePath</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">includePath</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t612" class="pln">            <span class="com"># Since we know where the input file came from,</span><span class="strut">&nbsp;</span></p>
+<p id="t613" class="pln">            <span class="com"># push its directory onto the include path.</span><span class="strut">&nbsp;</span></p>
+<p id="t614" class="stm mis">            <span class="nam">self</span><span class="op">.</span><span class="nam">addToIncludePath</span><span class="op">(</span><span class="op">[</span><span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">dirname</span><span class="op">(</span><span class="nam">sFile</span><span class="op">)</span><span class="op">]</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t615" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t616" class="pln">            <span class="com"># How we process the file depends on where the output is going.</span><span class="strut">&nbsp;</span></p>
+<p id="t617" class="stm mis">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sOutputName</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t618" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">processFile</span><span class="op">(</span><span class="nam">sFile</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sOutputName</span><span class="op">,</span> <span class="nam">sFile</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t619" class="stm mis">            <span class="key">elif</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">bReplace</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t620" class="pln">                <span class="com"># We want to replace the cog file with the output,</span><span class="strut">&nbsp;</span></p>
+<p id="t621" class="pln">                <span class="com"># but only if they differ.</span><span class="strut">&nbsp;</span></p>
+<p id="t622" class="stm mis">                <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">verbosity</span> <span class="op">>=</span> <span class="num">2</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t623" class="stm mis">                    <span class="nam">self</span><span class="op">.</span><span class="nam">prout</span><span class="op">(</span><span class="str">"Cogging %s"</span> <span class="op">%</span> <span class="nam">sFile</span><span class="op">,</span> <span class="nam">end</span><span class="op">=</span><span class="str">""</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t624" class="stm mis">                    <span class="nam">bNeedNewline</span> <span class="op">=</span> <span class="nam">True</span><span class="strut">&nbsp;</span></p>
+<p id="t625" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t626" class="stm mis">                <span class="key">try</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t627" class="stm mis">                    <span class="nam">fOldFile</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">openInputFile</span><span class="op">(</span><span class="nam">sFile</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t628" class="stm mis">                    <span class="nam">sOldText</span> <span class="op">=</span> <span class="nam">fOldFile</span><span class="op">.</span><span class="nam">read</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t629" class="stm mis">                    <span class="nam">fOldFile</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t630" class="stm mis">                    <span class="nam">sNewText</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">processString</span><span class="op">(</span><span class="nam">sOldText</span><span class="op">,</span> <span class="nam">fname</span><span class="op">=</span><span class="nam">sFile</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t631" class="stm mis">                    <span class="key">if</span> <span class="nam">sOldText</span> <span class="op">!=</span> <span class="nam">sNewText</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t632" class="stm mis">                        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">verbosity</span> <span class="op">>=</span> <span class="num">1</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t633" class="stm mis">                            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">verbosity</span> <span class="op">&lt;</span> <span class="num">2</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t634" class="stm mis">                                <span class="nam">self</span><span class="op">.</span><span class="nam">prout</span><span class="op">(</span><span class="str">"Cogging %s"</span> <span class="op">%</span> <span class="nam">sFile</span><span class="op">,</span> <span class="nam">end</span><span class="op">=</span><span class="str">""</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t635" class="stm mis">                            <span class="nam">self</span><span class="op">.</span><span class="nam">prout</span><span class="op">(</span><span class="str">"  (changed)"</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t636" class="stm mis">                            <span class="nam">bNeedNewline</span> <span class="op">=</span> <span class="nam">False</span><span class="strut">&nbsp;</span></p>
+<p id="t637" class="stm mis">                        <span class="nam">self</span><span class="op">.</span><span class="nam">replaceFile</span><span class="op">(</span><span class="nam">sFile</span><span class="op">,</span> <span class="nam">sNewText</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t638" class="pln">                <span class="key">finally</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t639" class="pln">                    <span class="com"># The try-finally block is so we can print a partial line</span><span class="strut">&nbsp;</span></p>
+<p id="t640" class="pln">                    <span class="com"># with the name of the file, and print (changed) on the</span><span class="strut">&nbsp;</span></p>
+<p id="t641" class="pln">                    <span class="com"># same line, but also make sure to break the line before</span><span class="strut">&nbsp;</span></p>
+<p id="t642" class="pln">                    <span class="com"># any traceback.</span><span class="strut">&nbsp;</span></p>
+<p id="t643" class="stm mis">                    <span class="key">if</span> <span class="nam">bNeedNewline</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t644" class="stm mis">                        <span class="nam">self</span><span class="op">.</span><span class="nam">prout</span><span class="op">(</span><span class="str">""</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t645" class="pln">            <span class="key">else</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t646" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">processFile</span><span class="op">(</span><span class="nam">sFile</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">stdout</span><span class="op">,</span> <span class="nam">sFile</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t647" class="pln">        <span class="key">finally</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t648" class="stm mis">            <span class="nam">self</span><span class="op">.</span><span class="nam">restoreIncludePath</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t649" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t650" class="stm run hide_run">    <span class="key">def</span> <span class="nam">processFileList</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">sFileList</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t651" class="pln">        <span class="str">""" Process the files in a file list.</span><span class="strut">&nbsp;</span></p>
+<p id="t652" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
+<p id="t653" class="stm mis">        <span class="nam">flist</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">openInputFile</span><span class="op">(</span><span class="nam">sFileList</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t654" class="stm mis">        <span class="nam">lines</span> <span class="op">=</span> <span class="nam">flist</span><span class="op">.</span><span class="nam">readlines</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t655" class="stm mis">        <span class="nam">flist</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t656" class="stm mis">        <span class="key">for</span> <span class="nam">l</span> <span class="key">in</span> <span class="nam">lines</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t657" class="pln">            <span class="com"># Use shlex to parse the line like a shell.</span><span class="strut">&nbsp;</span></p>
+<p id="t658" class="stm mis">            <span class="nam">lex</span> <span class="op">=</span> <span class="nam">shlex</span><span class="op">.</span><span class="nam">shlex</span><span class="op">(</span><span class="nam">l</span><span class="op">,</span> <span class="nam">posix</span><span class="op">=</span><span class="nam">True</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t659" class="stm mis">            <span class="nam">lex</span><span class="op">.</span><span class="nam">whitespace_split</span> <span class="op">=</span> <span class="nam">True</span><span class="strut">&nbsp;</span></p>
+<p id="t660" class="stm mis">            <span class="nam">lex</span><span class="op">.</span><span class="nam">commenters</span> <span class="op">=</span> <span class="str">'#'</span><span class="strut">&nbsp;</span></p>
+<p id="t661" class="pln">            <span class="com"># No escapes, so that backslash can be part of the path</span><span class="strut">&nbsp;</span></p>
+<p id="t662" class="stm mis">            <span class="nam">lex</span><span class="op">.</span><span class="nam">escape</span> <span class="op">=</span> <span class="str">''</span><span class="strut">&nbsp;</span></p>
+<p id="t663" class="stm mis">            <span class="nam">args</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="nam">lex</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t664" class="stm mis">            <span class="key">if</span> <span class="nam">args</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t665" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">processArguments</span><span class="op">(</span><span class="nam">args</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t666" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t667" class="stm run hide_run">    <span class="key">def</span> <span class="nam">processArguments</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">args</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t668" class="pln">        <span class="str">""" Process one command-line.</span><span class="strut">&nbsp;</span></p>
+<p id="t669" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
+<p id="t670" class="stm mis">        <span class="nam">saved_options</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="strut">&nbsp;</span></p>
+<p id="t671" class="stm mis">        <span class="nam">self</span><span class="op">.</span><span class="nam">options</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">clone</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t672" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t673" class="stm mis">        <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">parseArgs</span><span class="op">(</span><span class="nam">args</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">]</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t674" class="stm mis">        <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">validate</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t675" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t676" class="stm mis">        <span class="key">if</span> <span class="nam">args</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">==</span> <span class="str">'@'</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t677" class="stm mis">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">sOutputName</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t678" class="stm mis">                <span class="key">raise</span> <span class="nam">CogUsageError</span><span class="op">(</span><span class="str">"Can't use -o with @file"</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t679" class="stm mis">            <span class="nam">self</span><span class="op">.</span><span class="nam">processFileList</span><span class="op">(</span><span class="nam">args</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">]</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t680" class="pln">        <span class="key">else</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t681" class="stm mis">            <span class="nam">self</span><span class="op">.</span><span class="nam">processOneFile</span><span class="op">(</span><span class="nam">args</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
 <p id="t682" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t683" class="stm run hide_run">    <span class="key">def</span> <span class="nam">callableMain</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">argv</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t684" class="pln">        <span class="str">""" All of command-line cog, but in a callable form.</span><span class="strut">&nbsp;</span></p>
-<p id="t685" class="pln"><span class="str">            This is used by main.</span><span class="strut">&nbsp;</span></p>
-<p id="t686" class="pln"><span class="str">            argv is the equivalent of sys.argv.</span><span class="strut">&nbsp;</span></p>
-<p id="t687" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
-<p id="t688" class="stm mis">        <span class="nam">argv</span> <span class="op">=</span> <span class="nam">argv</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">]</span><span class="strut">&nbsp;</span></p>
-<p id="t689" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t690" class="pln">        <span class="com"># Provide help if asked for anywhere in the command line.</span><span class="strut">&nbsp;</span></p>
-<p id="t691" class="stm mis">        <span class="key">if</span> <span class="str">'-?'</span> <span class="key">in</span> <span class="nam">argv</span> <span class="key">or</span> <span class="str">'-h'</span> <span class="key">in</span> <span class="nam">argv</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t692" class="stm mis">            <span class="nam">self</span><span class="op">.</span><span class="nam">prerr</span><span class="op">(</span><span class="nam">usage</span><span class="op">,</span> <span class="nam">end</span><span class="op">=</span><span class="str">""</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t693" class="stm mis">            <span class="key">return</span><span class="strut">&nbsp;</span></p>
-<p id="t694" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t695" class="stm mis">        <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">parseArgs</span><span class="op">(</span><span class="nam">argv</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t696" class="stm mis">        <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">validate</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t697" class="stm mis">        <span class="nam">self</span><span class="op">.</span><span class="nam">_fixEndOutputPatterns</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t698" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t699" class="stm mis">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">bShowVersion</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t700" class="stm mis">            <span class="nam">self</span><span class="op">.</span><span class="nam">prout</span><span class="op">(</span><span class="str">"Cog version %s"</span> <span class="op">%</span> <span class="nam">__version__</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t701" class="stm mis">            <span class="key">return</span><span class="strut">&nbsp;</span></p>
-<p id="t702" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t703" class="stm mis">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">args</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t704" class="stm mis">            <span class="key">for</span> <span class="nam">a</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">args</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t705" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">processArguments</span><span class="op">(</span><span class="op">[</span><span class="nam">a</span><span class="op">]</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t706" class="pln">        <span class="key">else</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t707" class="stm mis">            <span class="key">raise</span> <span class="nam">CogUsageError</span><span class="op">(</span><span class="str">"No files to process"</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t708" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t709" class="stm run hide_run">    <span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">argv</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t710" class="pln">        <span class="str">""" Handle the command-line execution for cog.</span><span class="strut">&nbsp;</span></p>
-<p id="t711" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
-<p id="t712" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t713" class="stm mis">        <span class="key">try</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t714" class="stm mis">            <span class="nam">self</span><span class="op">.</span><span class="nam">callableMain</span><span class="op">(</span><span class="nam">argv</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t715" class="stm mis">            <span class="key">return</span> <span class="num">0</span><span class="strut">&nbsp;</span></p>
-<p id="t716" class="stm mis">        <span class="key">except</span> <span class="nam">CogUsageError</span> <span class="key">as</span> <span class="nam">err</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t717" class="stm mis">            <span class="nam">self</span><span class="op">.</span><span class="nam">prerr</span><span class="op">(</span><span class="nam">err</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t718" class="stm mis">            <span class="nam">self</span><span class="op">.</span><span class="nam">prerr</span><span class="op">(</span><span class="str">"(for help use -?)"</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t719" class="stm mis">            <span class="key">return</span> <span class="num">2</span><span class="strut">&nbsp;</span></p>
-<p id="t720" class="stm mis">        <span class="key">except</span> <span class="nam">CogGeneratedError</span> <span class="key">as</span> <span class="nam">err</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t721" class="stm mis">            <span class="nam">self</span><span class="op">.</span><span class="nam">prerr</span><span class="op">(</span><span class="str">"Error: %s"</span> <span class="op">%</span> <span class="nam">err</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t722" class="stm mis">            <span class="key">return</span> <span class="num">3</span><span class="strut">&nbsp;</span></p>
-<p id="t723" class="stm mis">        <span class="key">except</span> <span class="nam">CogError</span> <span class="key">as</span> <span class="nam">err</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t724" class="stm mis">            <span class="nam">self</span><span class="op">.</span><span class="nam">prerr</span><span class="op">(</span><span class="nam">err</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t725" class="stm mis">            <span class="key">return</span> <span class="num">1</span><span class="strut">&nbsp;</span></p>
-<p id="t726" class="stm mis">        <span class="key">except</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
-<p id="t727" class="stm mis">            <span class="nam">traceback</span><span class="op">.</span><span class="nam">print_exc</span><span class="op">(</span><span class="nam">None</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">stderr</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
-<p id="t728" class="stm mis">            <span class="key">return</span> <span class="num">1</span><span class="strut">&nbsp;</span></p>
-<p id="t729" class="pln"><span class="strut">&nbsp;</span></p>
-<p id="t730" class="pln"><span class="com"># History:</span><span class="strut">&nbsp;</span></p>
-<p id="t731" class="pln"><span class="com"># 20040210: First public version.</span><span class="strut">&nbsp;</span></p>
-<p id="t732" class="pln"><span class="com"># 20040220: Text preceding the start and end marker are removed from Python lines.</span><span class="strut">&nbsp;</span></p>
-<p id="t733" class="pln"><span class="com">#           -v option on the command line shows the version.</span><span class="strut">&nbsp;</span></p>
-<p id="t734" class="pln"><span class="com"># 20040311: Make sure the last line of output is properly ended with a newline.</span><span class="strut">&nbsp;</span></p>
-<p id="t735" class="pln"><span class="com"># 20040605: Fixed some blank line handling in cog.</span><span class="strut">&nbsp;</span></p>
-<p id="t736" class="pln"><span class="com">#           Fixed problems with assigning to xml elements in handyxml.</span><span class="strut">&nbsp;</span></p>
-<p id="t737" class="pln"><span class="com"># 20040621: Changed all line-ends to LF from CRLF.</span><span class="strut">&nbsp;</span></p>
-<p id="t738" class="pln"><span class="com"># 20041002: Refactor some option handling to simplify unittesting the options.</span><span class="strut">&nbsp;</span></p>
-<p id="t739" class="pln"><span class="com"># 20041118: cog.out and cog.outl have optional string arguments.</span><span class="strut">&nbsp;</span></p>
-<p id="t740" class="pln"><span class="com"># 20041119: File names weren't being properly passed around for warnings, etc.</span><span class="strut">&nbsp;</span></p>
-<p id="t741" class="pln"><span class="com"># 20041122: Added cog.firstLineNum: a property with the line number of the [[[cog line.</span><span class="strut">&nbsp;</span></p>
-<p id="t742" class="pln"><span class="com">#           Added cog.inFile and cog.outFile: the names of the input and output file.</span><span class="strut">&nbsp;</span></p>
-<p id="t743" class="pln"><span class="com"># 20041218: Single-line cog generators, with start marker and end marker on</span><span class="strut">&nbsp;</span></p>
-<p id="t744" class="pln"><span class="com">#           the same line.</span><span class="strut">&nbsp;</span></p>
-<p id="t745" class="pln"><span class="com"># 20041230: Keep a single globals dict for all the code fragments in a single</span><span class="strut">&nbsp;</span></p>
-<p id="t746" class="pln"><span class="com">#           file so they can share state.</span><span class="strut">&nbsp;</span></p>
-<p id="t747" class="pln"><span class="com"># 20050206: Added the -x switch to remove all generated output.</span><span class="strut">&nbsp;</span></p>
-<p id="t748" class="pln"><span class="com"># 20050218: Now code can be on the marker lines as well.</span><span class="strut">&nbsp;</span></p>
-<p id="t749" class="pln"><span class="com"># 20050219: Added -c switch to checksum the output so that edits can be</span><span class="strut">&nbsp;</span></p>
-<p id="t750" class="pln"><span class="com">#           detected before they are obliterated.</span><span class="strut">&nbsp;</span></p>
-<p id="t751" class="pln"><span class="com"># 20050521: Added cog.error, contributed by Alexander Belchenko.</span><span class="strut">&nbsp;</span></p>
-<p id="t752" class="pln"><span class="com"># 20050720: Added code deletion and settable globals contributed by Blake Winton.</span><span class="strut">&nbsp;</span></p>
-<p id="t753" class="pln"><span class="com"># 20050724: Many tweaks to improve code coverage.</span><span class="strut">&nbsp;</span></p>
-<p id="t754" class="pln"><span class="com"># 20050726: Error messages are now printed with no traceback.</span><span class="strut">&nbsp;</span></p>
-<p id="t755" class="pln"><span class="com">#           Code can no longer appear on the marker lines,</span><span class="strut">&nbsp;</span></p>
-<p id="t756" class="pln"><span class="com">#               except for single-line style.</span><span class="strut">&nbsp;</span></p>
-<p id="t757" class="pln"><span class="com">#           -z allows omission of the [[[end]]] marker, and it will be assumed</span><span class="strut">&nbsp;</span></p>
-<p id="t758" class="pln"><span class="com">#               at the end of the file.</span><span class="strut">&nbsp;</span></p>
-<p id="t759" class="pln"><span class="com"># 20050729: Refactor option parsing into a separate class, in preparation for</span><span class="strut">&nbsp;</span></p>
-<p id="t760" class="pln"><span class="com">#               future features.</span><span class="strut">&nbsp;</span></p>
-<p id="t761" class="pln"><span class="com"># 20050805: The cogmodule.path wasn't being properly maintained.</span><span class="strut">&nbsp;</span></p>
-<p id="t762" class="pln"><span class="com"># 20050808: Added the -D option to define a global value.</span><span class="strut">&nbsp;</span></p>
-<p id="t763" class="pln"><span class="com"># 20050810: The %s in the -w command is dealt with more robustly.</span><span class="strut">&nbsp;</span></p>
-<p id="t764" class="pln"><span class="com">#           Added the -s option to suffix output lines with a marker.</span><span class="strut">&nbsp;</span></p>
-<p id="t765" class="pln"><span class="com"># 20050817: Now @files can have arguments on each line to change the cog's</span><span class="strut">&nbsp;</span></p>
-<p id="t766" class="pln"><span class="com">#               behavior for that line.</span><span class="strut">&nbsp;</span></p>
-<p id="t767" class="pln"><span class="com"># 20051006: Version 2.0</span><span class="strut">&nbsp;</span></p>
-<p id="t768" class="pln"><span class="com"># 20080521: -U options lets you create Unix newlines on Windows.  Thanks,</span><span class="strut">&nbsp;</span></p>
-<p id="t769" class="pln"><span class="com">#               Alexander Belchenko.</span><span class="strut">&nbsp;</span></p>
-<p id="t770" class="pln"><span class="com"># 20080522: It's now ok to have -d with output to stdout, and now we validate</span><span class="strut">&nbsp;</span></p>
-<p id="t771" class="pln"><span class="com">#               the args after each line of an @file.</span><span class="strut">&nbsp;</span></p>
-<p id="t772" class="pln"><span class="com"># 20090520: Use hashlib where it's available, to avoid a warning.</span><span class="strut">&nbsp;</span></p>
-<p id="t773" class="pln"><span class="com">#           Use the builtin compile() instead of compiler, for Jython.</span><span class="strut">&nbsp;</span></p>
-<p id="t774" class="pln"><span class="com">#           Explicitly close files we opened, Jython likes this.</span><span class="strut">&nbsp;</span></p>
-<p id="t775" class="pln"><span class="com"># 20120205: Port to Python 3.  Lowest supported version is 2.6.</span><span class="strut">&nbsp;</span></p>
-<p id="t776" class="pln"><span class="com"># 20150104: --markers option added by Doug Hellmann.</span><span class="strut">&nbsp;</span></p>
-<p id="t777" class="pln"><span class="com"># 20150104: -n ENCODING option added by Petr Gladkiy.</span><span class="strut">&nbsp;</span></p>
-<p id="t778" class="pln"><span class="com"># 20150107: Added --verbose to control what files get listed.</span><span class="strut">&nbsp;</span></p>
-<p id="t779" class="pln"><span class="com"># 20150111: Version 2.4</span><span class="strut">&nbsp;</span></p>
-<p id="t780" class="pln"><span class="com"># 20160213: v2.5: -o makes needed directories, thanks Jean-Fran&#231;ois Giraud.</span><span class="strut">&nbsp;</span></p>
-<p id="t781" class="pln"><span class="com"># 20161019: Added a LICENSE.txt file.</span><span class="strut">&nbsp;</span></p>
+<p id="t683" class="stm mis">        <span class="nam">self</span><span class="op">.</span><span class="nam">options</span> <span class="op">=</span> <span class="nam">saved_options</span><span class="strut">&nbsp;</span></p>
+<p id="t684" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t685" class="stm run hide_run">    <span class="key">def</span> <span class="nam">callableMain</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">argv</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t686" class="pln">        <span class="str">""" All of command-line cog, but in a callable form.</span><span class="strut">&nbsp;</span></p>
+<p id="t687" class="pln"><span class="str">            This is used by main.</span><span class="strut">&nbsp;</span></p>
+<p id="t688" class="pln"><span class="str">            argv is the equivalent of sys.argv.</span><span class="strut">&nbsp;</span></p>
+<p id="t689" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
+<p id="t690" class="stm mis">        <span class="nam">argv</span> <span class="op">=</span> <span class="nam">argv</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">]</span><span class="strut">&nbsp;</span></p>
+<p id="t691" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t692" class="pln">        <span class="com"># Provide help if asked for anywhere in the command line.</span><span class="strut">&nbsp;</span></p>
+<p id="t693" class="stm mis">        <span class="key">if</span> <span class="str">'-?'</span> <span class="key">in</span> <span class="nam">argv</span> <span class="key">or</span> <span class="str">'-h'</span> <span class="key">in</span> <span class="nam">argv</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t694" class="stm mis">            <span class="nam">self</span><span class="op">.</span><span class="nam">prerr</span><span class="op">(</span><span class="nam">usage</span><span class="op">,</span> <span class="nam">end</span><span class="op">=</span><span class="str">""</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t695" class="stm mis">            <span class="key">return</span><span class="strut">&nbsp;</span></p>
+<p id="t696" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t697" class="stm mis">        <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">parseArgs</span><span class="op">(</span><span class="nam">argv</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t698" class="stm mis">        <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">validate</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t699" class="stm mis">        <span class="nam">self</span><span class="op">.</span><span class="nam">_fixEndOutputPatterns</span><span class="op">(</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t700" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t701" class="stm mis">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">bShowVersion</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t702" class="stm mis">            <span class="nam">self</span><span class="op">.</span><span class="nam">prout</span><span class="op">(</span><span class="str">"Cog version %s"</span> <span class="op">%</span> <span class="nam">__version__</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t703" class="stm mis">            <span class="key">return</span><span class="strut">&nbsp;</span></p>
+<p id="t704" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t705" class="stm mis">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">args</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t706" class="stm mis">            <span class="key">for</span> <span class="nam">a</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">options</span><span class="op">.</span><span class="nam">args</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t707" class="stm mis">                <span class="nam">self</span><span class="op">.</span><span class="nam">processArguments</span><span class="op">(</span><span class="op">[</span><span class="nam">a</span><span class="op">]</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t708" class="pln">        <span class="key">else</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t709" class="stm mis">            <span class="key">raise</span> <span class="nam">CogUsageError</span><span class="op">(</span><span class="str">"No files to process"</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t710" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t711" class="stm run hide_run">    <span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">argv</span><span class="op">)</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t712" class="pln">        <span class="str">""" Handle the command-line execution for cog.</span><span class="strut">&nbsp;</span></p>
+<p id="t713" class="pln"><span class="str">        """</span><span class="strut">&nbsp;</span></p>
+<p id="t714" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t715" class="stm mis">        <span class="key">try</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t716" class="stm mis">            <span class="nam">self</span><span class="op">.</span><span class="nam">callableMain</span><span class="op">(</span><span class="nam">argv</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t717" class="stm mis">            <span class="key">return</span> <span class="num">0</span><span class="strut">&nbsp;</span></p>
+<p id="t718" class="stm mis">        <span class="key">except</span> <span class="nam">CogUsageError</span> <span class="key">as</span> <span class="nam">err</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t719" class="stm mis">            <span class="nam">self</span><span class="op">.</span><span class="nam">prerr</span><span class="op">(</span><span class="nam">err</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t720" class="stm mis">            <span class="nam">self</span><span class="op">.</span><span class="nam">prerr</span><span class="op">(</span><span class="str">"(for help use -?)"</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t721" class="stm mis">            <span class="key">return</span> <span class="num">2</span><span class="strut">&nbsp;</span></p>
+<p id="t722" class="stm mis">        <span class="key">except</span> <span class="nam">CogGeneratedError</span> <span class="key">as</span> <span class="nam">err</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t723" class="stm mis">            <span class="nam">self</span><span class="op">.</span><span class="nam">prerr</span><span class="op">(</span><span class="str">"Error: %s"</span> <span class="op">%</span> <span class="nam">err</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t724" class="stm mis">            <span class="key">return</span> <span class="num">3</span><span class="strut">&nbsp;</span></p>
+<p id="t725" class="stm mis">        <span class="key">except</span> <span class="nam">CogError</span> <span class="key">as</span> <span class="nam">err</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t726" class="stm mis">            <span class="nam">self</span><span class="op">.</span><span class="nam">prerr</span><span class="op">(</span><span class="nam">err</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t727" class="stm mis">            <span class="key">return</span> <span class="num">1</span><span class="strut">&nbsp;</span></p>
+<p id="t728" class="stm mis">        <span class="key">except</span><span class="op">:</span><span class="strut">&nbsp;</span></p>
+<p id="t729" class="stm mis">            <span class="nam">traceback</span><span class="op">.</span><span class="nam">print_exc</span><span class="op">(</span><span class="nam">None</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">stderr</span><span class="op">)</span><span class="strut">&nbsp;</span></p>
+<p id="t730" class="stm mis">            <span class="key">return</span> <span class="num">1</span><span class="strut">&nbsp;</span></p>
+<p id="t731" class="pln"><span class="strut">&nbsp;</span></p>
+<p id="t732" class="pln"><span class="com"># History:</span><span class="strut">&nbsp;</span></p>
+<p id="t733" class="pln"><span class="com"># 20040210: First public version.</span><span class="strut">&nbsp;</span></p>
+<p id="t734" class="pln"><span class="com"># 20040220: Text preceding the start and end marker are removed from Python lines.</span><span class="strut">&nbsp;</span></p>
+<p id="t735" class="pln"><span class="com">#           -v option on the command line shows the version.</span><span class="strut">&nbsp;</span></p>
+<p id="t736" class="pln"><span class="com"># 20040311: Make sure the last line of output is properly ended with a newline.</span><span class="strut">&nbsp;</span></p>
+<p id="t737" class="pln"><span class="com"># 20040605: Fixed some blank line handling in cog.</span><span class="strut">&nbsp;</span></p>
+<p id="t738" class="pln"><span class="com">#           Fixed problems with assigning to xml elements in handyxml.</span><span class="strut">&nbsp;</span></p>
+<p id="t739" class="pln"><span class="com"># 20040621: Changed all line-ends to LF from CRLF.</span><span class="strut">&nbsp;</span></p>
+<p id="t740" class="pln"><span class="com"># 20041002: Refactor some option handling to simplify unittesting the options.</span><span class="strut">&nbsp;</span></p>
+<p id="t741" class="pln"><span class="com"># 20041118: cog.out and cog.outl have optional string arguments.</span><span class="strut">&nbsp;</span></p>
+<p id="t742" class="pln"><span class="com"># 20041119: File names weren't being properly passed around for warnings, etc.</span><span class="strut">&nbsp;</span></p>
+<p id="t743" class="pln"><span class="com"># 20041122: Added cog.firstLineNum: a property with the line number of the [[[cog line.</span><span class="strut">&nbsp;</span></p>
+<p id="t744" class="pln"><span class="com">#           Added cog.inFile and cog.outFile: the names of the input and output file.</span><span class="strut">&nbsp;</span></p>
+<p id="t745" class="pln"><span class="com"># 20041218: Single-line cog generators, with start marker and end marker on</span><span class="strut">&nbsp;</span></p>
+<p id="t746" class="pln"><span class="com">#           the same line.</span><span class="strut">&nbsp;</span></p>
+<p id="t747" class="pln"><span class="com"># 20041230: Keep a single globals dict for all the code fragments in a single</span><span class="strut">&nbsp;</span></p>
+<p id="t748" class="pln"><span class="com">#           file so they can share state.</span><span class="strut">&nbsp;</span></p>
+<p id="t749" class="pln"><span class="com"># 20050206: Added the -x switch to remove all generated output.</span><span class="strut">&nbsp;</span></p>
+<p id="t750" class="pln"><span class="com"># 20050218: Now code can be on the marker lines as well.</span><span class="strut">&nbsp;</span></p>
+<p id="t751" class="pln"><span class="com"># 20050219: Added -c switch to checksum the output so that edits can be</span><span class="strut">&nbsp;</span></p>
+<p id="t752" class="pln"><span class="com">#           detected before they are obliterated.</span><span class="strut">&nbsp;</span></p>
+<p id="t753" class="pln"><span class="com"># 20050521: Added cog.error, contributed by Alexander Belchenko.</span><span class="strut">&nbsp;</span></p>
+<p id="t754" class="pln"><span class="com"># 20050720: Added code deletion and settable globals contributed by Blake Winton.</span><span class="strut">&nbsp;</span></p>
+<p id="t755" class="pln"><span class="com"># 20050724: Many tweaks to improve code coverage.</span><span class="strut">&nbsp;</span></p>
+<p id="t756" class="pln"><span class="com"># 20050726: Error messages are now printed with no traceback.</span><span class="strut">&nbsp;</span></p>
+<p id="t757" class="pln"><span class="com">#           Code can no longer appear on the marker lines,</span><span class="strut">&nbsp;</span></p>
+<p id="t758" class="pln"><span class="com">#               except for single-line style.</span><span class="strut">&nbsp;</span></p>
+<p id="t759" class="pln"><span class="com">#           -z allows omission of the [[[end]]] marker, and it will be assumed</span><span class="strut">&nbsp;</span></p>
+<p id="t760" class="pln"><span class="com">#               at the end of the file.</span><span class="strut">&nbsp;</span></p>
+<p id="t761" class="pln"><span class="com"># 20050729: Refactor option parsing into a separate class, in preparation for</span><span class="strut">&nbsp;</span></p>
+<p id="t762" class="pln"><span class="com">#               future features.</span><span class="strut">&nbsp;</span></p>
+<p id="t763" class="pln"><span class="com"># 20050805: The cogmodule.path wasn't being properly maintained.</span><span class="strut">&nbsp;</span></p>
+<p id="t764" class="pln"><span class="com"># 20050808: Added the -D option to define a global value.</span><span class="strut">&nbsp;</span></p>
+<p id="t765" class="pln"><span class="com"># 20050810: The %s in the -w command is dealt with more robustly.</span><span class="strut">&nbsp;</span></p>
+<p id="t766" class="pln"><span class="com">#           Added the -s option to suffix output lines with a marker.</span><span class="strut">&nbsp;</span></p>
+<p id="t767" class="pln"><span class="com"># 20050817: Now @files can have arguments on each line to change the cog's</span><span class="strut">&nbsp;</span></p>
+<p id="t768" class="pln"><span class="com">#               behavior for that line.</span><span class="strut">&nbsp;</span></p>
+<p id="t769" class="pln"><span class="com"># 20051006: Version 2.0</span><span class="strut">&nbsp;</span></p>
+<p id="t770" class="pln"><span class="com"># 20080521: -U options lets you create Unix newlines on Windows.  Thanks,</span><span class="strut">&nbsp;</span></p>
+<p id="t771" class="pln"><span class="com">#               Alexander Belchenko.</span><span class="strut">&nbsp;</span></p>
+<p id="t772" class="pln"><span class="com"># 20080522: It's now ok to have -d with output to stdout, and now we validate</span><span class="strut">&nbsp;</span></p>
+<p id="t773" class="pln"><span class="com">#               the args after each line of an @file.</span><span class="strut">&nbsp;</span></p>
+<p id="t774" class="pln"><span class="com"># 20090520: Use hashlib where it's available, to avoid a warning.</span><span class="strut">&nbsp;</span></p>
+<p id="t775" class="pln"><span class="com">#           Use the builtin compile() instead of compiler, for Jython.</span><span class="strut">&nbsp;</span></p>
+<p id="t776" class="pln"><span class="com">#           Explicitly close files we opened, Jython likes this.</span><span class="strut">&nbsp;</span></p>
+<p id="t777" class="pln"><span class="com"># 20120205: Port to Python 3.  Lowest supported version is 2.6.</span><span class="strut">&nbsp;</span></p>
+<p id="t778" class="pln"><span class="com"># 20150104: --markers option added by Doug Hellmann.</span><span class="strut">&nbsp;</span></p>
+<p id="t779" class="pln"><span class="com"># 20150104: -n ENCODING option added by Petr Gladkiy.</span><span class="strut">&nbsp;</span></p>
+<p id="t780" class="pln"><span class="com"># 20150107: Added --verbose to control what files get listed.</span><span class="strut">&nbsp;</span></p>
+<p id="t781" class="pln"><span class="com"># 20150111: Version 2.4</span><span class="strut">&nbsp;</span></p>
+<p id="t782" class="pln"><span class="com"># 20160213: v2.5: -o makes needed directories, thanks Jean-Fran&#231;ois Giraud.</span><span class="strut">&nbsp;</span></p>
+<p id="t783" class="pln"><span class="com"># 20161019: Added a LICENSE.txt file.</span><span class="strut">&nbsp;</span></p>
 
             </td>
         </tr>
@@ -1643,8 +1647,8 @@
 <div id="footer">
     <div class="content">
         <p>
-            <a class="nav" href="index.html">&#xab; index</a> &nbsp; &nbsp; <a class="nav" href="https://coverage.readthedocs.io">coverage.py v4.3.2</a>,
-            created at 2017-01-16 18:24
+            <a class="nav" href="index.html">&#xab; index</a> &nbsp; &nbsp; <a class="nav" href="https://coverage.readthedocs.io">coverage.py v4.4</a>,
+            created at 2017-05-07 19:06
         </p>
     </div>
 </div>