Update SCM commands to add/remove files.

In Git, for example:

    doorstop edit REQ --> git add PATH/TO/REQ999.yml
    doorstop add REQ --> git add PATH/TO/REQ999.yml
    doorstop remove REQ999 --> git rm PATH/TO/REQ999.yml

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TODO:

- [x] call edit where appropriate
- [x] call add where appropriate
- [x] call delete where appropriate (move item/document delete into the decorator)
- [x] add tests for expected calls (split up class for those that do and do not require a VCS)
- [x] remove coverage pragmas for ignored paths
- [x] check for unnecessary test decorators