This makes the lock management on the index a little bit broader,
having a number of routines hold the lock across looking up the
item to be modified and actually making the modification.  Still
not true thread safety, but more pure index modifications are now
safe which allows the simple cases (such as starting up a diff
while index modifications are underway) safe enough to get the
snapshot without hitting allocation problems.

As part of this, I simplified the allocation of index entries to
use a flex array and just put the path at the end of the index
entry.  This makes every entry self-contained and makes it a
little easier to feel sure that pointers to strings aren't
being accidentally copied and freed while other references are
still being held.

This makes the index iterator honor the GIT_ITERATOR_IGNORE_CASE
and GIT_ITERATOR_DONT_IGNORE_CASE flags without modifying the
index data itself.  To take advantage of this, I had to export a
number of the internal index entry comparison functions.  I also
wrote some new tests to exercise the capability.

The usefulness of these helpers came up for me while debugging
some of the iterator changes that I was making, so since they
have also been requested (albeit indirectly) I thought I'd include
them.

It will form part of the subject line and should thus be one line.

With the new submodule cache validity checks, we generally don't
need to call git_submodule_reload_all to have up-to-date submodule
data.  Some tests are still calling it where I want to actually
test that it can be called safely and doesn't break anything, but
mostly it is not needed.

This also expands some of the existing submodule tests to cover
some variants on the behavior that was already being tested.