Repo reinit fix + enhanced test coverage

Topic/refs fromglob

indexer: start parsing input data immediately

Currently, the first call of git_indexer_stream_add adds the data to the
underlying pack file and opens it for later use, but doesn't start
parsing the already available data.
This means, git_indexer_stream_finalize only works if
git_indexer_stream_add was called at least twice. Kill this limitation
by parsing available data immediately.

Fix MSVC compilation errors

When the repository was reinitialized, every configuration change in repo_init_config() was directly performed against the file on the filesystem. However, a previous version of the configuration had previously been loaded in memory and attached to the repository, in repo_init_reinit().

The repository was unaware of the change and the stale cached version of the configuration never refreshed.

Branch foreach

Cleanup

fix crash issue on mingw caused by variable argument list type promotion.

1. compile warning:

D:\libgit2.git\src\win32\posix_w32.c: In function 'p_open':
D:\libgit2.git\src\win32\posix_w32.c:235:10: warning: 'mode_t' is promoted to 'int' when passed through '...' [enabled by default]
D:\libgit2.git\src\win32\posix_w32.c:235:10: note: (so you should pass 'int' not 'mode_t' to 'va_arg')
D:\libgit2.git\src\win32\posix_w32.c:235:10: note: if this code is reached, the program will abort

2. test crash.

3. the above two issues are same root cause. please see http://www.eskimo.com/~scs/cclass/int/sx11c.html

The second call to assert_config_entry_on_init_bytype is cleaned up by
the main cleanup function, but that overwrites the first _repo. Make
sure that one doesn't leak.

The call to repo_init_reinit already takes care of opening the
repository and giving us a git_repository object to give to the
caller. There is no need to call git_repository_open again.

Fix Makefile.emebed for mingw32

Don't need unix/*.c for windows, don't need wildcard for regex.c

Revparse fixup

otherwise we can't compile the native parts of the rugged gem on Windows

When the creation of one iterator fails, we need to free the prefix
and possibly one of the iterators. Make sure we do so.

If we find several objects with the same prefix, we need to free the
memory where we stored the earlier object. Keep track of the raw.data
pointer across read_prefix calls and free it if we find another
object.

Make index add/append support core.filemode flag