Clear up some of the various "find" functions and the snapshot
API naming to be things I like more.

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.

This surrounds any function that mutates the entries vector with
a mutex so it can be safely snapshotted.

Again, laying groundwork for some index iterator changes, this
contains a bunch of code refactorings for index internals that
should make it easier down the line to add locking around index
modifications.  Also this removes the redundant prefix_position
function and fixes some potential memory leaks.

This makes submodule cache refresh actually look at the timestamps
from the data sources for submodules and reload as needed if they
have changed since the last refresh.

This fixes a number of warnings with the Windows 64-bit build
including a test failure in test_repo_message__message where an
invalid pointer to a git_buf was being used.

This cleans up some additional issues.  The main change is that
on a filesystem that doesn't support mode bits, libgit2 will now
create new blobs with GIT_FILEMODE_BLOB always instead of being
at the mercy to the filesystem driver to report executable or not.
This means that if "core.filemode" lies and claims that filemode
is not supported, then we will ignore the executable bit from the
filesystem.  Previously we would have allowed it.

This adds an option to the new git_repository_reset_filesystem to
recurse through submodules if desired.  There may be other types
of APIs that would like a "recurse submodules" option, but this
one is particularly useful.

This also has a number of cleanups, etc., for related things
including trying to give better error messages when problems come
up from the filesystem.  For example, the FAT filesystem driver on
MacOS appears to return errno EINVAL if you attempt to write a
filename with invalid UTF-8 in it.  We try to capture that with a
better error message now.