Without this option, we would not be able to catch exec bit changes.

The idea...sometimes, a filemode is user-specified via an
explicit git_index_entry.  In this case, believe the user, always.

Sometimes, it is instead built up by statting the file system.  In
those cases, go with the existing logic we have to determine
whether the file system supports all filemodes and symlinks, and
make the best guess.

On file systems which have full filemode and symlink support, this
commit should make no difference.  On others (most notably Windows),
this will fix problems things like:
* git_index_add and git_index_add_frombuffer() should be believed.
* As a consequence, git_checkout_tree should make the filemodes in
the index match the ones in the tree.
* And diffs with GIT_DIFF_UPDATE_INDEX don't write the wrong filemodes.
* And merges, and probably other downstream stuff now fixed, too.

This makes my previous changes to checkout.c unnecessary,
so they are now reverted.

Also, added a test for index_entry permissions from git_index_add
and git_index_add_frombuffer, both of which failed before these changes.

This function is meant to simulate what git does in the reset command,
so we should include the reflog message in that.

The signature for the reflog is not something which changes
dynamically. Almost all uses will be NULL, since we want for the
repository's default identity to be used, making it noise.

In order to allow for changing the identity, we instead provide
git_repository_set_ident() and git_repository_ident() which allow a user
to override the choice of signature.

git_index_add_frombuffer enables now to store a memory buffer in the odb
and to store an entry in the index directly if the index is attached to a
repository.

Introduce `git_indexwriter`, to allow us to lock the index while
performing additional operations, then complete the write (or abort,
unlocking the index).