Exclude skills dir in manifest

[cdce8p]

Fix check-manifest be explicitly excluding the skills dir.
Followup to #22072

Build failure: https://github.com/mypyc/mypy_mypyc-wheels/actions/runs/37029975663/job/110914062986#step:5:34

[github-actions]

Diff from mypy_primer, showing the effect of this PR on open source code:

scipy-stubs (https://github.com/scipy/scipy-stubs)
- scipy-stubs/cluster/hierarchy/_hierarchy_impl.pyi:6: note: See https://mypy.readthedocs.io/en/stable/running_mypy.html#missing-imports
+ tests/spatial/test__plotutils.pyi:7: note: See https://mypy.readthedocs.io/en/stable/running_mypy.html#missing-imports
- tests/misc/test_submodules_empty.pyi:3: note: See https://mypy.readthedocs.io/en/stable/running_mypy.html#missing-imports

[ilevkivskyi]

Btw @hauntsaninja it looks like some dependencies are missing for scipy-stubs in mypy_primer.