Some function calls in the new "apply" test suite were missing the
checks whether they succeeded as expected. Fix this by adding the
missing `cl_git_pass` wrappers.

Move the location option to an argument, out of the options structure.
This allows the options structure to be re-used for functions that don't
need to know the location, since it's implicit in their functionality.
For example, `git_apply_tree` should not take a location, but is
expected to take all the other options.

Test that a mode change is reflected in the working directory or index.

Patch application need not be on an unmodified file; applying to an
already changed file is supported provided the patch still applies
cleanly.  Add tests that modifies the contents of a file then applies
the patch and ensures that the patch applies cleanly, and the original
changes are also kept.

Ensure that we can apply to the working directory or the index when the
application target is modified, so long as there are not conflicting
changes to the items.

Ensure that when a patch application fails (due to a conflict in the
working directory, for example) that we do not half-apply the patch or
otherwise leave the working directory dirty.

This is rather obvious in our current apply implementation (we do a two
step process: one to create the post-image and one to check it out) but
this test is a safety net for future refactoring or improvements.

Ensure that we can apply a patch to the working directory, even to files
that are modified in the index (as long as the working directory
contents match the preimage - such that the working directory is
unmodified from HEAD).

Ensure that by default, when using GIT_APPLY_LOCATION_WORKDIR, that
patch application does not update the index, only the working directory.