AWY: add results suffix to a few files

[davemfish]

A few intermediate file outputs were missing the suffix. Based on the variable names, perhaps these files used to be temporary and that's why they didn't get the suffix. But they are no longer temporary.

I also corrected a couple minor bugs in the output spec for this model (intermediate folder not nested within output) and in the carbon model.

Fixes #1517

Checklist

• Updated HISTORY.rst and link to any relevant issue (if these changes are user-facing)
• Updated the user's guide (if needed)
• Tested the Workbench UI (if relevant)

[emlys]

Great, thanks @davemfish!