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

Trees, indices and repos need to be freed

For the diff-index tests, the diff_more test will run multiple
times. Reset the expect_idx counter after each test in order to
allow this.

Conflicts:
	tests-clay/clay.h
	tests-clay/clay_main.c

Signed-off-by: Carlos Martín Nieto <carlos@cmartin.tk>
Signed-off-by: Vicent Marti <tanoku@gmail.com>

There's no difference between `_free` and `_close` semantics: keep
everything with the same name to avoid confusions.

The ownership semantics have been changed all over the library to be
consistent. There are no more "borrowed" or duplicated references.

Main changes:

	- `git_repository_open2` and `3` have been dropped.

	- Added setters and getters to hotswap all the repository owned
	objects:

		`git_repository_index`
		`git_repository_set_index`
		`git_repository_odb`
		`git_repository_set_odb`
		`git_repository_config`
		`git_repository_set_config`
		`git_repository_workdir`
		`git_repository_set_workdir`

	Now working directories/index files/ODBs and so on can be
	hot-swapped after creating a repository and between operations.

	- All these objects now have proper ownership semantics with
	refcounting: they all require freeing after they are no longer
	needed (the repository always keeps its internal reference).

	- Repository open and initialization has been updated to keep in
	mind the configuration files. Bare repositories are now always
	detected, and a default config file is created on init.

	- All the tests affected by these changes have been dropped from the
	old test suite and ported to the new one.