CL/git: add format version 1

The original nmbug format (now called version 0) creates 1
subdirectory of 'tags/' per message. This causes problems for more
than (roughly) 100k messages.

Version 1 introduces 2 layers of hashed directories. This scheme was
chose to balance the number of subdirectories with the number of extra
directories (and git objects) created via hashing.

This should be upward compatible in the sense that old repositories
will continue to work with the updated notmuch-git.