move non-standard command line options that change execution behavior to cwltool specific CWL extensions

( As suggested by @tetron )

Standard interface is https://github.com/common-workflow-language/common-workflow-language/pull/278/files#diff-ee814a9c027fc9750beb075c283a973c

Some options could be added as standardized but optional command line flags.

Non-standard options to consider
- [ ] `--basedir`
- [ ] `--no-container`
- [ ] `--preserve-environment`
- [ ] `--preserve-entire-environment`
- [ ] `--rm-container`
- [ ] `--leave-container`
- [ ] `--tmpdir-prefix`
- [ ] `--tmp-outdir-prefix`
- [ ] `--cachedir`
- [ ] `--rm-tmpdir`
- [ ] `--leave-tmpdir`
- [ ] `--move-outputs`
- [ ] `--leave-outputs`
- [ ] `--copy-outputs`
- [ ] `--enable-pull`
- [ ] `--disable-pull`
- [ ] `--rdf-serializer`
- [ ] `--eval-timeout`
- [ ] `--print-rdf`
- [ ] `--print-dot`
- [ ] `--print-pre`
- [ ] `--print-deps`
- [ ] `--print-input-deps`
- [ ] `--pack`
- [ ] `--version`
- [ ] `--validate`
- [ ] `--print-supported-versions`
- [ ] `--strict`
- [ ] `--non-strict`
- [ ] `--skip-schemas`
- [ ] `--verbose`
- [ ] `--debug`
- [ ] `--tool-help`
- [ ] `--relative-deps`
- [ ] `--enable-dev`
- [ ] `--enable-ext`
- [ ] `--default-container`
- [ ] `--no-match-user`
- [ ] `--disable-net`
- [ ] `--custom-net`
- [ ] `--enable-ga4gh-tool-registry`
- [ ] `--disable-ga4gh-tool-registry`
- [ ] `--add-ga4gh-tool-registry`
- [ ] `--on-error`
- [ ] `--compute-checksum`
- [ ] `--no-compute-checksum`
- [ ] `--relax-path-checks`
- [ ] `--make-template`
- [ ] `--force-docker-pull`