Review the use of environment variables in the `rose-app.conf` files

Review the use of environment variables in the rose-app.conf files.

For each variable:
- If the variable should be configurable by the user (to answer this, put the list to @alistairsellar)
- Then add it to the `rose-app.conf` file so that it's editable in the GUI
- Otherwise define in task for that app in the `flow.cylc` file (or at a higher level in `flow.cylc` if needed by multiple tasks)

Original context below:

> 1. Is the `[env]` section not required in `CMEW/app/configure_for/rose-app.conf`? @alistairsellar should these be present from a `rose edit` perspective? Or should things only be added to the `[env]` section when they can be edited by users?

Hi @ehogan. On (1) the workflow runs OK without this `[env]` section. Good question on `rose edit`. I don't know if there is a recommended approach to this, but think it would be undesirable to expose these in the GUI since the parametrisation would break if users edited them. So I think it's preferable as things stand in the current branch.

_Originally posted by @alistairsellar in https://github.com/MetOffice/CMEW/issues/161#issuecomment-1914584880_