Therapist

- **MAJOR BUG FIX**: Therapist now handles copied file correctly.
Previously it would fail or overwrite the contents of copied files.

- Fix an issue with detecting which action modified files.
- Added the ability to configure shortcuts.
- When `--include-untracked` and `--use-tracked-files` are used
together the files are correctly selected.

- Fix a second issue with false positives in detecting files modified
by actions.

- Fixes an issue with false positives in detecting files modified by
actions.

- Added the `--stage-modified-files` flag to the `run` command. When
this is used any files modified by the actions will be staged after
running.
- Added the `--no-stage-modified-files` flag to the `install` command.
This prevents the default hook behaviour of staging any files
modified by the hook while it's running.

- Added the `--fix` flag to the `run` command to automatically fix
issues when possible.
- New `fix` parameter for
[action definitions](https://therapist.readthedocs.io/en/v1.4.0/configuration.html#action-definitions).
- Added the `--fix` flag to the `install` command to configure the hook
to use `--fix` with `run`.