Fix manifest filtering for different ecosystems #3580

Job	Run time
test-matrix (ubuntu-20.04)	9m 8s
test-matrix (self-hosted, macos, arm64)	1m 19s
clippy (ubuntu-20.04)	4m 44s
oldstable (ubuntu-20.04)	5m 53s
clippy (self-hosted, macos, arm64)	49s
rustfmt	15s
oldstable (self-hosted, macos, arm64)	51s
all-features (ubuntu-20.04)	9m 42s
all-features (self-hosted, macos, arm64)	1m 24s
deno-checks	17s
shellcheck	4s
test	1s
	34m 27s

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