Finalize package management documentation

[casella]

The section of the User's Guide dealing with the package manager and conversion scripts needs to be finalized for 1.19.0.

PR #8146 significantly expands the original text. Information about the OMEdit GUI is still missing and should be added before the release.

[casella]

There are three remaining open points here, as I understand

• reinstate the package manager mos script in the documentation, as suggested by @sjoelund here. I don't think it is really necessary in that section of the documentation, I'm not sure if it is needed elsewhere
• fix Resolving conflicts with loaded libraries when opening new ones #8183, so that it is also consistent with the documentation
• add cross-references to the API documentation, I need help to do that because I have no clue how this can be done

[casella]

See #8263

[adeas31]

reinstate the package manager mos script in the documentation, as suggested by @sjoelund here. I don't think it is really necessary in that section of the documentation, I'm not sure if it is needed elsewhere

I don't think there is any need to add the mos-script back. The latest documentation by @casella doesn't use any API call so setting the environment is not needed.

add cross-references to the API documentation, I need help to do that because I have no clue how this can be done

Done.