Provide git_indexwriter_init_for_operation for the common locking
pattern in merge, rebase, revert and cherry-pick.

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.

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

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.

win32: limit the mode to `_wopen`/`_waccess`

Win32 generally ignores Unix-like mode bits that don't make any
sense on the platform (eg `0644` makes no sense to Windows).  But
WINE complains loudly when presented with POSIXy bits.  Remove them.

(Thanks @phkelley)

Reinit `reader` pointer after reading included config file

Fix build warning on Android

Always do a time_t cast on st_mtime. st_mtime on Android is not
the type of time_t but has the same meaning which is the number
of seconds past epoch.

Check rebase options version on public entry points

Fixes #2869. If included file includes more files, it may reallocate
cfg_file->readers, hence invalidate not only `r` pointer, but `result`
pointer as well.

It fails at least on my computer, though it may depend on some unpredictable
factors (say, will realloc() extend the memory segment in place, or it will
allocate new memory).

Checkout performance

Remove stale reflog namespace directory before branch creation

Ensure we can make a repo at the root of the filesystem

Add libssh2's library and include directories.

Large merge perf test.

Update some third-party copyrights

Fix doc comment formatting

Speed up AppVeyor builds.

AppVeyor build machines come with Python 2.7 and CMake 2.8 pre-installed and in the PATH.

repository: parse init.templatedir as a path

This is a path so we must use the path getter so we get the tilde
expansion done.

Update clar to d17c7f6

Don't try to strip trailing paths from the root directory on
Windows (trying to create `C:` will fail).

`p_stat` calls `git_win32_path_from_utf8`, which canonicalizes the
path.  Do not further try to modify the path, else we trim the
trailing slash from a root directory and try to access `C:` instead
of `C:/`.

Test to ensure that we can create a repository at the filesystem
root.  Introduces a new test environment variable,
`GITTEST_INVASIVE_FILESYSTEM` for tests that do terrible things like
escaping the clar sandbox and writing to the root directory.  It is
expected that the CI builds will enable this but that normal people
would not want this.

Handle 8dot3 filenames being disabled on Win32

for-each-ref example: initialize libgit2 in main