ontology extractor sees 3 of 9 aprender-ci-tools subcommands, graph reports 6 false ledgerOrphans #5181

Found in seat review of #5175 (head acec3ba).

After the ten aprender-ci-tools rows were ledgered in docs/audits/surface_audit.csv (#5170), the regenerated contracts/contracts.nt marks 6 of its surfaces as ledgerOrphans. The ontology extractor discovers only 3 of the 9 subcommands in crates/aprender-ci-tools/src/main.rs, so rows that do exist in the binary read as orphans.

Expected: every subcommand the binary dispatches is extracted, and the ci-tools rows produce 0 orphans.

Refs #5170