Update scenario.yaml results for nightly tests

[khaeru]

This PR updates nightly test expected values.

It contains a subset of the changes in #669, supersedes #688, and closes #671.

How to review

Per #688 (comment):

1. Push a commit temporarily enabling these lines:
   

   message_ix/.github/workflows/nightly.yaml

   Lines 6 to 8 in 8e701a4

   	# Uncomment these two lines for debugging, but leave them commented on 'main'
   	# pull_request:
   	# branches: [ main ]

2. Follow the resulting "nightly" run.
3. Once it passes, confirming the new values:
   • Approve.
   • Force-push the branch to drop the temporary commit. (This can also be done by pushing a second commit that comments the 2 lines again, if the branch is to be squash-merged.)
   • Merge.

PR checklist

• Continuous integration checks all ✅
• [ ] Add or expand tests; coverage checks both ✅
• [ ] Add, expand, or update documentation. N/A; CI changes only.
• [ ] Update release notes.

[codecov]

Codecov Report

Merging #689 (04afc14) into main (8e701a4) will not change coverage.
The diff coverage is n/a.

@@          Coverage Diff          @@
##            main    #689   +/-   ##
=====================================
  Coverage   93.5%   93.5%           
=====================================
  Files         44      44           
  Lines       3514    3514           
=====================================
  Hits        3286    3286           
  Misses       228     228           

[khaeru]

https://github.com/iiasa/message_ix/actions/runs/4044981970/jobs/6955825538#step:10:6901 passed:

=========================== short test summary info ============================
PASSED message_ix/tests/test_nightly.py::test_scenario[CD_Links_SSP2_baseline]
PASSED message_ix/tests/test_nightly.py::test_scenario[CD_Links_SSP2_v2_1000]
=========== 2 passed, 157 deselected, 1 warning in 730.32s (0:12:10) ===========