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cleanup: CLI simplify pass, correctness fixes, core dedups, scan split, docs sync (−587 net lines) #357

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Run time

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Job	Run time
test (windows-latest)	12m 32s
test-release	20m 55s
coverage	3m 49s
e2e-docker (maven)	4m 49s
test (ubuntu-latest)	5m 51s
setup-matrix (npm)	3m 48s
setup-matrix (cargo)	3m 5s
coverage-docker (maven)	5m 53s
lint-ecosystems	6s
e2e-docker (pypi)	4m 35s
coverage-docker (composer)	5m 28s
e2e-docker (gem)	4m 24s
e2e-docker (golang)	4m 27s
e2e-docker (deno)	4m 21s
setup-matrix (pypi)	4m 21s
setup-matrix (maven)	4m 35s
e2e-docker (composer)	4m 17s
setup-matrix (gem)	3m 10s
setup-matrix (composer)	3m 15s
setup-matrix (golang)	3m 2s
clippy	25s
test (macos-latest)	4m 1s
setup-matrix (deno)	3m 15s
setup-matrix (nuget)	3m 29s
dispatch-tests	11s
coverage-docker (npm)	5m 18s
e2e-docker (cargo)	4m 26s
e2e-docker (nuget)	4m 36s
coverage-docker (pypi)	5m 39s
coverage-docker (golang)	5m 21s
coverage-docker (cargo)	5m 41s
e2e-docker (npm)	4m 31s
coverage-docker (deno)	5m 27s
coverage-docker (nuget)	5m 54s
coverage-docker (gem)	5m 25s
coverage-merge	0s
e2e	0s
	2h 50m 22s