friendlier repo.init_at API

is_bare is now optional and defaults to false, same as git init. It's also
parsed as normal Ruby truthy value instead of type checked for True
or False, so more readable calls like this can be made

   Rugged::Repository.init_at('~/repository', :bare)
Remove unexisting command repo.hash.
s/rugged/repo in Rugged::Commit section.
tag.target_type returns a symbol, not string.
s/rugged/repo in TreeBuilder section.
No method get_entry for index.
Fix Rugged::Reference part.

1. ref.type returns a symbol instead of string.
2. ref.set_target instead of ref.target=
3. Reference entry has keys id_old and id_new instead of oid_*
repo instead of @repo in Branch section.
Merge pull request #174 from DawidJanczak/readme_update

Readme update
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