This makes the API for commiting or discarding changes the same as for
references.

This lock/unlock pair allows for the cller to lock a configuration file
to avoid concurrent operations.

It also allows for a transactional approach to updating a configuration
file. If multiple updates must be made atomically, they can be done
while the config is locked.

When a configuration file is locked, any updates made to it will be done
to the in-memory copy of the file. This allows for multiple updates to
happen while we hold the lock, preventing races during complex
config-file manipulation.

Resolve documentation warnings

Allow adding a submodule through git_index_add_bypath

refdb: delete a ref's reflog upon deletion