builtin-commit: fix partial-commit support

builtin-commit: fix partial-commit support

When making a partial-commit, we need to prepare two index
files, one to be used to write out the tree to be committed
(temporary index) and the other to be used as the index file
after the commit is made.

The temporary index needs to be initialized to HEAD and then all
the named paths on the command line need to be staged on top of
the index.  For this, running add_files_to_cache() that compares
what is in the index and the paths given from the command line
is not enough -- the comparison will miss the paths that the
user previously ran "git add" to the index since the HEAD
because the index reset to the HEAD would not know about them.
The index file needs to get the same modification done when
preparing the temporary index as described above.

This implementation mimics the behaviour of the scripted
version of git-commit.  It first runs overlay_tree_on_cache(),
which was stolen from ls-files with the earlier change, to get
the list of paths that the user can potentially mean, and then
uses pathspec_match() to find which ones the user meant.  This
list of paths is used to update both the temporary and the real
index file.

Additional fixes are:

 - read the index file after pre-commit hook returns, as the
   hook can modify it to affect the contents of the commit.

 - remove the temporary index file .git/next-index-* after
   commit is done or aborted.

 - run post-commit hook with the real index file to be used
   after the commit (previously it gave the temporary commit if
   a partial commit was made).

 - resurrect the safety mechanism to refuse partial commits
   during a merge to match the scripted version.

Signed-off-by: Junio C Hamano <gitster@pobox.com>