Tasks for CWLProv

- [x] `make diff_pylint_report` is clean
- [ ] Test with `toil-cwl-runner`, does this break anything?
- [ ] move extra Python dependencies to an extra, add code to remind the user to install them if `--provenance is called`
- [x] @mr-c to review type hints
- [x] remove use of `hasattr`
- [x] add raw logs
- [x] test with aligner workflow
- [x] deal with directory structures
- [ ] add annotations (EDAM if available) for input data artefact entity in provenance file
- [ ] pylint mostly clean `cwltool/provenance.py` and `tests/test_provenance.py`
- [x] refactor out global `relativised_input_object`
- [ ] resolve TODO and FIXME or move to issues or another document
- [x] make sure snapshot only contains definition and job files
- [ ] in case of failure, generate provenance files anyway.
- [ ] record docker container image id and labels
- [ ] record kernel version
```
docker inspect --format='{{.Id }}' --type image microscaling/microscaling # Image sha256
docker inspect --format='{{ json .Config.Labels }}' --type image microscaling/microscaling
```
- [ ] confirm `--provenance` & `--cachedir` coexistence