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.

When applying to the index (using `GIT_APPLY_LOCATION_INDEX`), ensure
that items modified in the working directory do not conflict with the
application.

Add a test that adds a new file, and another that removes a file when
applying using `GIT_APPLY_LOCATION_INDEX` to ensure that they work.

Test a simple patch application with `GIT_APPLY_LOCATION_INDEX`, which
emulates `git apply --cached`.