Replace the `GITERR` values with a `const int` to deprecate error
values.

Move to the `git_error` name in error-related functions, deprecating the
`giterr` functions.  This means, for example, that `giterr_last` is now
`git_error_last`.  The old names are retained for compatibility.

This only updates the public API; internal API and function usage
remains unchanged.

Allow credential and certificate checking callbacks to return
GIT_PASSTHROUGH, indicating that they do not want to act.
Introduce this to support in both the http and ssh callbacks.
Additionally, enable the same mechanism for certificate validation.

This is most useful to disambiguate any meaning in the publicly exposed
credential and certificate functions (`git_transport_smart_credentials`
and `git_transport_smart_certificate_check`) but it may be more
generally useful for callers to be able to defer back to libgit2.

Return `GIT_EAPPLYFAIL` on patch application failure so that users can
determine that patch application failed due to a malformed/conflicting
patch by looking at the error code.

Documentation fixes

When the index is dirty, return GIT_EINDEXDIRTY so that consumers can
identify the exact problem programatically.