Update CLI help docs

[IAlibay]

Related to #796

This PR only updates the help docs to reflect the current status of the CLI.

Checklist

• [ ] Added a news entry

Developers certificate of origin

• [x] I certify that this contribution is covered by the MIT License here and the Developer Certificate of Origin at https://developercertificate.org/.

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 91.40%. Comparing base (223e49a) to head (e284dd4).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #797 +/- ## ========================================== - Coverage 94.12% 91.40% -2.72% ========================================== Files 133 133 Lines 9767 9767 ========================================== - Hits 9193 8928 -265 - Misses 574 839 +265 ``` | [Flag](https://app.codecov.io/gh/OpenFreeEnergy/openfe/pull/797/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OpenFreeEnergy) | Coverage Δ | | |---|---|---| | [fast-tests](https://app.codecov.io/gh/OpenFreeEnergy/openfe/pull/797/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OpenFreeEnergy) | `91.40% <ø> (?)` | | | [slow-tests](https://app.codecov.io/gh/OpenFreeEnergy/openfe/pull/797/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OpenFreeEnergy) | `?` | | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=OpenFreeEnergy#carryforward-flags-in-the-pull-request-comment) to find out more.

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