Registry hygiene (any repo built from this kit)

Keep the SN → SR → LLR → TC spine (and the off-spine PB/PART/ASSET/REPO/CMP registries) clean: zero orphans, no duplicate/malformed ids, valid schema. Run the right check for where you are, then read and fix the findings.

Which command, when

# Always-valid floor (pre-commit + check.py at G1): duplicate/malformed ids
# and CSV structure (every registry data row parses to the header's column count).
python scripts/trace.py --strict-integrity

# Full orphan check (aim for orphans=0 before any gate).
python scripts/trace.py --strict

# G2+: also reject leftover template example rows (ids ending -000).
python scripts/trace.py --strict --no-placeholders

# G3: required fields non-empty + closed Verification/Tier vocabularies + Verified.
python scripts/trace.py --strict --no-placeholders --strict-schema --require-verified

scripts/check.py (or scripts/check.{sh,ps1}) runs the gate-appropriate set automatically from the active gate in docs/gate — prefer it for a full gate run; call trace.py directly to iterate on a specific finding.

Reading findings

• orphan — a row not joined end-to-end. Common causes: an SR with no LLR/TC yet (fine early; a real orphan at G2+), a Refs/SN-Refs/SR-Refs id that points at nothing, a TC that verifies no real id. Fix the back-link, don't delete the evidence.
• integrity (duplicate/malformed id, or a CSV structure break) — two rows share an id, an id doesn't match the PREFIX-### shape, or a data row parses to more/fewer columns than its header (almost always an unquoted comma in a Permutations set or free-text cell — quote the cell). Renumber the duplicate; fix the malformed id; quote the offending cell. The structure sweep covers every *.csv under docs/requirements/ and docs/test/, including registries trace.py never joins (interfaces, project-added ones).
• schema (--strict-schema) — a required field is empty, or a Verification/Tier value is outside the closed vocabulary (Test|Demonstration|Inspection|Analysis|Manual|Attest|Critique; Smoke|Full|Release). Fill the field or correct the value.
• placeholder (--no-placeholders) — a template -000 example row survived; delete it once real rows exist.
• AC advisory (WARNING (advisory), warn-only — never fails a run) — an AcceptanceCriteria uses a comparative term (identical / indistinguishable / equivalent / "same as" / matches) without naming its predicate. Pin it: say identical in what, judged how — or accept the wording knowingly at the G1 consistency review (process.md §4).
• LLR status-coherence advisory (WARNING (advisory), warn-only — never fails a run) — an LLR reads below Verified while every TC that cites it is Verified, so the evidence to lift it already exists. Fix: edit the LLR's Status cell to Verified (registries are hand-owned — no generator writes them back). It never gates: LLR status is non-gating under the derived-gate model (the SR's Verified drives G2→G3), so a lagging LLR is a readout drift, not a coverage hole.

Verify the fix

Re-run the same command; it must print orphans=0 (and exit 0). trace.py regenerates docs/test/report.md — the readable matrix — so review that too. Off-spine registries (PB/PART/ASSET/REPO/CMP; legacy MOD read too) are integrity-checked only plus their declared joins (PB Refs, REPO DelegatedSRs, CMP PartOf/SupersededBy + the primitives' Component tags); a valid inert -000 placeholder there never blocks a gate.