Repository.xs: Adjust merge API
Repository.xs: Added merge_base()
Tree.xs: Add merge()
Index.xs: Allow add() to take an Index::Entry object
Index.xs: Added additional Index methods

write_tree_to()
checkout()
entries()
add_conflict()
remove_conflict()
Index.xs: Index::Entry's should be tied to the repository, not the Index
Commit.xs: Cleanup
Commit.xs: Added merge()
Raw.xs: Added additional checkout options
Updated documentation
Changes: update