Move commit::apply_opts to store::apply_commit #297

[joepio]

Related Issues

closes #297

ToDo

• Move apply_changes from Commit to Resource::apply_commit
• Move the store specific code from apply_opts to Storelike and Db, where we index
• Get rid of add_atom_to_index functions in Storelike
• use sled::Batch

Checklist

• Add changelog entry linking to issue, describe API changes
• Add or update tests if needed
• Update docs if needed