Some fixes for external template support

Before, it was identical to the default template making it difficult
to check, if the proper template was copied an external template
test.

been properly copied.

This is a minimal effort to test whether the template really has
been used when creating an repo with external templates.

This is an intermin solution. While this essentially disables the
--shared flag feature, previously external templates did not work
at all. This change fixes the previously corrected, and since
then failing, repo_init__extended_with_template() test.

The problem is now documented in the source code comments.

The offset should be git_off_t, and we should check the return value
of the mutex lock function.

The indexer needs to call the packfile's free function so it takes care of
freeing the caches.

We still need to close the mwf descriptor manually so we can rename the
packfile into its final name on Windows.

Otherwise the template functionallity is not tested (as a TODO we
also shall test that the specified template really got copied).

Switch to specified branch during clone

Fixes #1232

Add a failing test for CRLF filters

This adds a git_buf_text_is_binary check to blobs before applying
filters when the blob data is being written to disk.

Match binary file check of core git in diff

Fix diff patch line number calculation

Core git just looks for NUL bytes in files when deciding about
is-binary inside diff (although it uses a better algorithm in
checkout, when deciding if CRLF conversion should be done).
Libgit2 was using the better algorithm in both places, but that
is causing some confusion.  For now, this makes diff just look
for NUL bytes to decide if a file is binary by content in diff.

This was just wrong.  Added a test that verifying patch line
numbers even for hunks further into a file and then fixed the
algorithm.  I needed to add a little extra state into the patch
so that I could track old and new file numbers independently,
but it should be okay.

This reverts commit f289f886, which
makes the tests fail on Windows. Revert until we can figure out a
solution.

Introduce EMERGECONFLICT

Introduce a delta base cache

Some regex warning fixes

It turns out the indexers have been ignoring the pack's free function
and leaking data. Plug that.

Currently limited to 16MB (like git) and to objects up to 1MB in
size.

refspec: prevent git_refspec__free() from segfaulting

Many delta bases are re-used. Cache them to avoid inflating the same
data repeatedly.

This version doesn't limit the amount of entries to store, so it can
end up using a considerable amound of memory.