Improve AGENTS.md and SKILLs#20
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The `references/` glob also caught documentation directories under each skill (.claude/skills/*/references/). Anchor the rule to the repo root so skill-internal references are tracked. Co-Authored-By: Claude Opus 4.7 (1M context) <[email protected]>
- Recognise `→ formalized: QuantumSystem.X.y` as a third concept tier above `→ mathlib:` on INDEX.md Key concepts bullets. The same `[UNVERIFIED]` loop in verify_mathlib_refs.py extracts both kinds and tags each worklist item with `kind` (mathlib | formalized). - Add gap-filler/scripts/issues.py with add / list / close subcommands, idempotent on (kind, slug, concept, candidate). `mark-unverified` opens one tracker entry per failure via subprocess so unresolved references survive across sessions; pass --no-issues to suppress. - Document the new tier in pdf-to-knowledge / web-to-knowledge SKILL.md and pdf-to-knowledge/references/output-format.md. Co-Authored-By: Claude Opus 4.7 (1M context) <[email protected]>
Earlier goals.yaml measured satisfaction via `concepts` matched against
INDEX.md bullets — a knowledge-coverage proxy, not real Lean
verification. Switch the truth source to `declarations`, scanned
directly from <lean-root>/**/*.lean.
- detect_gaps.py: bespoke YAML subset parser (block + flow `{}` /
`[]`); Lean scanner that tracks namespace / end stacks to build
fully-qualified declaration names; hard validation on malformed
goals.yaml; new --lean-root, --history-log, --no-history flags;
gaps-history.jsonl now records declarations_total /
declarations_verified.
- New goals.yaml schema: `declarations: [Lean.Path.foo]` is the
truth; `concepts: [bare-string | {name, sources: [{slug, anchor:
{kind: ref}}]}]` is informational hint for gap-filler. Coverage =
verified_decls / total_decls; an empty `declarations: []` slot
counts as one missing target so TODOs do not silently inflate
the score.
- Populate goals.yaml at the repo root with the 7 README highlights
plus the abstract-local-net SSA TODO; the scanner verifies 19/20
declarations against the current QuantumSystem tree (score 0.95).
- Update gap-filler SKILL.md "Side channels" and references/
workflow.md with the new schema and worked examples.
Co-Authored-By: Claude Opus 4.7 (1M context) <[email protected]>
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Part of #18