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fix: security and correctness hardening across API, tools, MCP, persistence, and gateways #645

Job	Run time
format	20s
markdown	13s
duplication	12s
module hygiene	2m 5s
deadcode	29s
vet	2m 14s
secrets	12s
security	-1s
smoke	-1s
test (race + coverage)	-1s
lint	-1s
fuzz (60s)	-1s
build (${{ matrix.goos }}/${{ matrix.goarch }})	0s
	5m 40s