Add git_buf_put_base64 to buffer API

The fix for fetching from empty repositories (22935b06 protocol:
don't store flushes; 2012-10-07) forgot to take into account the
deletion of the flush pkt in the HTTP transport. As a result, the HEAD
ref advertisement where we detect the remote's capabilities was
deleted instead. Fix this.

[GSoC] RFC: pack objects

Use khash instead of git.git's hashing algorithm.

Diff submodule tests and fixes

* tests-clar/status: remove an unused variable
* clone: fix -Wmaybe-uninitialized warning

Deploy git_repository_set_head()

The adds a test for the submodule diff capabilities and then
fixes a few bugs with how the output is generated.  It improves
the accuracy of OIDs in the diff delta object and makes the
submodule output more closely mirror the OIDs that will be used
by core git.

There are a few cases where diff should leave directories in
the diff list if we want to match core git, such as when the
directory contains a .git dir.  That feature was lost when I
introduced some of the new submodule handling.

This restores that and then fixes a couple of related to diff
output that are triggered by having diffs with directories in
them.

Also, this adds a new flag that can be passed to diff if you
want diff output to actually include the file content of any
untracked files.

Diff: Show submodule diff

Fix a bug where ignorecase wasn't applied to ignores

The reference is only needed inside the function. We mistakenly
increased the reference counter causing the ODB not to get freed and
leaking descriptors.

Storing flushes in the refs vector doesn't let us recognize when the
remote is empty, as we'd always introduce at least one element into
it. These flushes aren't necessary, so we can simply ignore them.

We don't have anything useful that we could do with that oid anyway (We
need to query the submodule for the HEAD commit instead).

Without this, the following code creates the error "Failed to read
descriptor: Is a directory" when run against the submod2 test-case:

    const char* oidstr = "873585b94bdeabccea991ea5e3ec1a277895b698";
    git_tree* tree = resolve_commit_oid_to_tree(g_repo, oidstr);
    git_diff_list* diff = NULL;
    cl_assert(tree);
    cl_git_pass(git_diff_workdir_to_tree(g_repo, NULL, tree, &diff));