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index: three missing lookup indexes made large-repo queries and warm take minutes #607

Job	Run time
build & typecheck	49s
what changed	6s
repo invariants	9s
engine (java)	10m 13s
engine (typescript)	9m 14s
engine (python)	3m 20s
engine (csharp)	4m 9s
engine (javascript)	5m 17s
pack @axiomcode/code-graph	0s
engines build on every platform	0s
e2e on ${{ matrix.target.platform }}	0s
CI	3s
	33m 20s