As we attempt to replicate a situation in which an older checkout has
put a file on disk with different filtering settings from us, set the
timestamp on the entry and file to a second before we're performing the
operation so the entry in the index counts as old.

This way we can test that we're not looking at the on-disk file when the
index has the entry and we detect it as clean.

It's not always obvious the mapping between stage level and
conflict-ness.  More importantly, this can lead otherwise sane
people to write constructs like `if (!git_index_entry_stage(entry))`,
which (while technically correct) is unreadable.

Provide a nice method to help avoid such messy thinking.

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.

Always lock the index when we begin the merge, before we write
any of the metdata files.  This prevents a race where another
client may run a commit after we have written the MERGE_HEAD but
before we have updated the index, which will produce a merge
commit that is treesame to one parent.  The merge will finish and
update the index and the resultant commit would not be a merge at
all.

Correct the merge failed cleanup test.  Merge data should not be
cleaned up on conflicts, only on actual failure.  And ORIG_HEAD
should not be removed at all.

Rename git_merge_head to git_annotated_commit, as it becomes used
in more operations than just merge.

Signed-off-by: Sven Strickroth <email@cs-ware.de>

git_checkout_index can now check out other git_index's (that are not
necessarily the repository index).  This allows checkout_index to use
the repository's index for stat cache information instead of the index
data being checked out.  git_merge and friends now check out their
indexes directly instead of trying to blend it into the running index.

git_merge_analysis will now return GIT_MERGE_CONFIG_NO_FASTFORWARD
when merge.ff=false and GIT_MERGE_CONFIG_FASTFORWARD_ONLY when
merge.ff=true