Group submodule functions under Repository.submodules

[jorio]

Following up on #1248 (comment), this PR implements a Submodules class that groups submodule functions in a Repository, much like Branches, References and RemoteCollection.

For backward compatibility, I turned the old functions into simple pass-throughs to the new class. Should we write unit tests for the deprecated versions?

[jdavid]

Great @jorio

Could you please:

• Remove submodule_status, submodule_cache_all and submodule_cache_clear ; these are new so no need to go through the deprecation process.
• In add_submodule, init_submodules, lookup_submodule and update_submodules : call warnings.warn(...) ; see pygit2/repository.py line 323
• Move the Submodules class to its own file submodules.py

Thanks!