[docs] + [cli] openfe atommapping

[IAlibay]

The CLI has an atommapping option which seems to no longer be advertised in when calling openfe --help.

However it is present in the docs: https://docs.openfree.energy/en/latest/guide/cli/cli_basics.html

1. Should atommaping be including in the help message? (I haven't seen a commit that specifically seemed to try to remove it)
2. If yes - let's add it back
3. If no - let's update the docs accordingly

[IAlibay]

This issue blocks OpenFreeEnergy/ExampleNotebooks#117

[richardjgowers]

it was made hidden in this PR: #414

I think it's probably something we should remove entirely, it was a fun idea that doesn't scale well

[IAlibay]

Re-opening: whilst the docs were dealt with, the atommapping CLI entry point still exists - if we don't want it then we should remove it.