This adds the ability for checkout to write to a target directory
instead of having to use the working directory of the repository.
This makes it easier to do exports of repository data and the like.

This is similar to, but not quite the same as, the --prefix option
to `git checkout-index` (this will always be treated as a directory
name, not just as a simple text prefix).

As part of this, the workdir iterator was extended to take the
path to the working directory as a parameter and fallback on the
git_repository_workdir result only if it's not specified.

Fixes #1332

This is a significant reorganization of the diff code to break it
into a set of more clearly distinct files and to document the new
organization.  Hopefully this will make the diff code easier to
understand and to extend.

This adds a new `git_diff_driver` object that looks of diff driver
information from the attributes and the config so that things like
function content in diff headers can be provided.  The full driver
spec is not implemented in the commit - this is focused on the
reorganization of the code and putting the driver hooks in place.

This also removes a few #includes from src/repository.h that were
overbroad, but as a result required extra #includes in a variety
of places since including src/repository.h no longer results in
pulling in the whole world.

1. internal iterators now return GIT_ITEROVER when you go past the
   last item in the iteration.
2. git_iterator_advance will "advance" to the first item in the
   iteration if it is called immediately after creating the
   iterator, which allows a simpler idiom for basic iteration.
3. if git_iterator_advance encounters an error reading data (e.g.
   a missing tree or an unreadable file), it returns the error
   but also attempts to advance past the invalid data to prevent
   an infinite loop.

Updated all tests and internal usage of iterators to account for
these new behaviors.

When attempting to create a workdir iterator for a bare repo,
don't leak the iterator structure.

Renamed the callback functions and made some minor rearrangements
to clean up the flow of some code.

This adds some hooks into the filesystem iterator so that the
workdir iterator can just become a wrapper around it.  Then we
remove most of the workdir iterator code and just have it augment
the filesystem iterator with skipping .git entries, updating the
ignore stack, and checking for submodules.

This adds a new variant iterator that is a raw filesystem iterator
for scanning directories from a root.  There is still more work to
do to blend this with the working directory iterator.

1. Fix sort order problem with submodules where "mod" was sorting
   after "mod-plus" because they were being sorted as "mod/" and
   "mod-plus/".  This involved pushing the "contains a .git entry"
   test significantly lower in the stack.
2. Reinstate behavior that a directory which contains a .git entry
   will be treated as a submodule during iteration even if it is
   not yet added to the .gitmodules.
3. Now that any directory containing .git is reported as submodule,
   we have to be more careful checking for GIT_EEXISTS when we
   do a submodule lookup, because that is the error code that is
   returned by git_submodule_lookup when you try to look up a
   directory containing .git that has no record in gitmodules or
   the index.

This updates the tree iterator internals to be more efficient.

The tree_iterator_entry objects are now kept as pointers that are
allocated from a git_pool, so that we may use git__tsort_r for
sorting (which is better than qsort, given that the tree is
likely mostly ordered already).

Those tree_iterator_entry objects now keep direct pointers to the
data they refer to instead of keeping indirect index values.  This
simplifies a lot of the data structure traversal code.

This also adds bsearch to find the start item position for range-
limited tree iterators, and is more explicit about using
git_path_cmp instead of reimplementing it.  The git_path_cmp
changed a bit to make it easier for tree_iterators to use it (but
it was barely being used previously, so not a big deal).

This adds a git_pool_free_array function that efficiently frees a
list of pool allocated pointers (which the tree_iterator keeps).
Also, added new tests for the git_pool free list functionality
that was not previously being tested (or used).