[red-knot] Fix bug where module resolution would not be invalidated if an entire package was deleted #30799

Job	Run time
Determine changes	9s
mkdocs	2m 26s
pre-commit	29s
cargo fmt	14s
python package	1m 10s
benchmarks	4m 46s
cargo build (msrv)	3m 3s
cargo clippy	1m 45s
cargo build (release)	4m 41s
cargo fuzz	4m 29s
cargo shear	25s
cargo test (wasm)	1m 6s
cargo test (linux)	3m 17s
cargo test (windows)	9m 26s
test scripts	58s
formatter instabilities and black similarity	0s
test ruff-lsp	25s
Fuzz the parser	0s
ecosystem	8m 53s
	47m 42s

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