Make Python tools work in CESM checkout

[samsrabin]

Our Python tools work in standalone CTSM checkouts, but @linniahawkins noticed that they don't—at least not all of them—in CESM checkouts. She specifically noticed this with subset_data, which looks for cime/ under clm/. For now, she's working around it with softlinks.

I think this would be fine to test solely on PRs—just make sure our Python system and unit tests pass under CESM checkouts in addition to the existing CTSM check.

[slevis-lmwg]

Mentioning #2658 as possibly related.

[slevis-lmwg]

Might the solution to #3580 work here, too?