Can't write checkpoints from coupled model

### Version

main

### Are there any linked Issues or Pull Requests?

#196

### What happened?

[https://code.metoffice.gov.uk/trac/lfric_apps/ticket/981](https://code.metoffice.gov.uk/trac/lfric_apps/ticket/981) broke restart capability with the coupled model. Previously it was possible to output checkpoints with the coupled model by including the fields in the XML file (it was never set up correctly to add the fields automatically) but the above ticket broke this.
FCM branches at the git_migration version exist here:
[https://code.metoffice.gov.uk/trac/lfric_apps/browser/main/branches/dev/timgraham/git_migration_fix_cpl_checkpoint](https://code.metoffice.gov.uk/trac/lfric_apps/browser/main/branches/dev/timgraham/git_migration_fix_cpl_checkpoint) and
[https://code.metoffice.gov.uk/trac/lfric/browser/LFRic/branches/dev/timgraham/git_migration_fix_cpl_chkpts]
(https://code.metoffice.gov.uk/trac/lfric/browser/LFRic/branches/dev/timgraham/git_migration_fix_cpl_chkpts)

### Relevant log output

```shell

```

The issue points to linked issue #196, Trac ticket 981, and two migration branches; start by comparing those references and branches to understand the coupled-model checkpoint regression. Done means restoring checkpoint output and restart capability for the coupled model, but the report names no file or test to run.

Written by the indexing model from the issue text.