fix dmypy namespace cache 20519

[SynapShift]

Summary

When dmypy reuses a fine-grained cache, a namespace-package ancestor can appear in State.ancestors without having a corresponding graph node. On a later unchanged run, find_reachable_changed_modules() indexed that missing node and crashed with KeyError.

Only enqueue dependencies and ancestors that are present in the graph. Add an end-to-end daemon regression test covering the original sequence: create a fine-grained cache containing an error, start dmypy from that cache, change a module below a namespace package, and run the daemon again without further changes.

Fixes #20519.

Tests

• python -m pytest -o addopts='' -q "mypy/test/testdaemon.py::DaemonSuite::daemon.test::testDaemonFineGrainedCacheNamespacePackage"
• python -m pytest -o addopts='' -q mypy/test/testfinegrainedcache.py — 538 passed, 227 skipped
• python -m ruff check mypy/dmypy_server.py
• python -m ruff format --check mypy/dmypy_server.py

[github-actions]

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

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