This fixes git_index_add and git_index_append to behave more like
core git, preserving old filemode data in the index when adding
and/or appending with core.filemode = false.

This also has placeholder support for core.symlinks and
core.ignorecase, but those flags are not implemented (well,
symlinks has partial support for preserving mode information in
the same way that git does, but it isn't tested).

File modes were both not being ignored properly on platforms
where they should be ignored, nor be diffed consistently on
platforms where they are supported.

This change adds a number of diff and status filemode change
tests.  This also makes sure that filemode-only changes are
included in the diff output when they occur and that filemode
changes are ignored successfully when core.filemode is false.

There is no code that automatically toggles core.filemode
based on the capabilities of the current platform, so the user
still needs to be careful in their .git/config file.

It can cause segfaults if the call didn't set an error

This updates to the latest clar which includes the helpers
`cl_assert_equal_s` and `cl_assert_equal_i`.  Convert the code
over to use those and remove the old libgit2-only helpers.

Add a new command `git_repository_open_ext` with extended options
that control how searching for a repository will be done.  The
existing `git_repository_open` and `git_repository_discover` are
reimplemented on top of it.  We may want to change the default
behavior of `git_repository_open` but this commit does not do that.

Improve support for "gitdir" files where the work dir is separate
from the repo and support for the "separate-git-dir" config.  Also,
add support for opening repos created with `git-new-workdir` script
(although I have only confirmed that they can be opened, not that
all functions work correctly).

There are also a few minor changes that came up:

- Fix `git_path_prettify` to allow in-place prettifying.

- Fix `git_path_root` to support backslashes on Win32.  This fix
  should help many repo open/discover scenarios - it is the one
  function called when opening before prettifying the path.

- Tweak `git_config_get_string` to set the "out" pointer to NULL
  if the config value is not found.  Allows some other cleanup.

- Fix a couple places that should have been calling
  `git_repository_config__weakptr` and were not.

- Fix `cl_git_sandbox_init` clar helper to support bare repos.

It turns out that commit 31e9cfc4cbcaf1b38cdd3dbe3282a8f57e5366a5
did not fix the GIT_USUSED behavior on all platforms.  This commit
walks through and really cleans things up more thoroughly, getting
rid of the unnecessary stuff.

To remove the use of some GIT_UNUSED, I ended up adding a couple
of new iterators for hashtables that allow you to iterator just
over keys or just over values.

In making this change, I found a bug in the clar tests (where we
were doing *count++ but meant to do (*count)++ to increment the
value).  I fixed that but then found the test failing because it
was not really using an empty repo.  So, I took some of the code
that I wrote for iterator testing and moved it to clar_helpers.c,
then made use of that to make it easier to open fixtures on a
per test basis even within a single test file.

This is a major reorganization of the diff code.  This changes
the diff functions to use the iterators for traversing the
content.  This allowed a lot of code to be simplified.  Also,
this moved the functions relating to outputting a diff into a
new file (diff_output.c).

This includes a number of other changes - adding utility
functions, extending iterators, etc. plus more tests for the
diff code.  This also takes the example diff.c program much
further in terms of emulating git-diff command line options.

This adds some initial unit tests for file filtering and fixes
some simple bugs in filter application.

Clay is the name of a programming language on the makings, and we want
to avoid confusions. Sorry for the huge diff!

This converts virtually all of the places that allocate GIT_PATH_MAX
buffers on the stack for manipulating paths to use git_buf objects
instead.  The patch is pretty careful not to touch the public API
for libgit2, so there are a few places that still use GIT_PATH_MAX.

This extends and changes some details of the git_buf implementation
to add a couple of extra functions and to make error handling easier.

This includes serious alterations to all the path.c functions, and
several of the fileops.c ones, too.  Also, there are a number of new
functions that parallel existing ones except that use a git_buf
instead of a stack-based buffer (such as git_config_find_global_r
that exists alongsize git_config_find_global).

This also modifies the win32 version of p_realpath to allocate whatever
buffer size is needed to accommodate the realpath instead of hardcoding
a GIT_PATH_MAX limit, but that change needs to be tested still.

This streamlines git_buf_join and removes the join-append behavior,
opting instead for a very compact join-replace of the git_buf contents.
The unit tests had to be updated to remove the join-append tests and
have a bunch more exhaustive tests added.

Add new functions to git_buf for:
* initializing a buffer from a string
* joining one or more strings onto a buffer with separators
* swapping two buffers in place
* extracting data from a git_buf (leaving it empty)

Also, make git_buf_free leave a git_buf back in its initted state,
and slightly tweak buffer allocation sizes and thresholds.

Finally, port unit tests to clay and extend with lots of new tests
for the various git_buf functions.

Comes with schu's stress tests for config files. Hopefully the diffs
will stay minimal from now on.