Three independent manifest fixes from Opus TOML + Sonnet TOML + Sonnet Markdown
audits.
1. TOML scope-capture (Sonnet TOML, HIGH)
_manifests/critic-anti-pattern.toml + critic-perf.toml had [references]
appearing AFTER [[handoff]] array-of-tables. Per TOML spec, this makes
[references] parse as a SUB-TABLE of the last [[handoff]] element, not as
a top-level table. All references in those manifests were silently
unreachable by the assembler's top-level resolver.
Moved [references] block before [[handoff]] in both files. Added 3-line
warning comment immediately above [[handoff]] explaining the TOML scope rule
to future editors.
2. Dangling physics-deriver in role bodies (Opus TOML, HIGH)
Group F earlier (commit baf5425) removed [[handoff]] blocks targeting
physics-deriver / patent-compliance / patent-researcher, but role text
strings + forbidden_domain arrays still referenced physics-deriver in:
- _manifests/ml-researcher.toml (lines 16, 41, 76, 89)
- _manifests/ml-implementer.toml (line 15)
- _manifests/infra-implementer.toml (line 16) — already scrubbed in P0
commit 94f31ee as part of EC2-ID strip; leaving for context
Replaced live mentions with "architect" (canonical fallback). Historical
comments documenting the prior removal kept intentionally — they are
documentation, not live references.
3. Wrong rule paths (Opus TOML, MEDIUM)
ml-researcher.toml + ml-implementer.toml referenced files that don't exist
under their stated paths:
- path:user-rules/specialized-node-training.md → cfc-specialized-nodes.md
- path:user-rules/observable-classification.md → paradigm-native-measurement.md
Fixed both paths in both files.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Phase 1 of substrate-unified-registry: move all references to user
home memory/rules out of plain strings and into content-addressable
path atoms. Public artefacts now contain opaque `{path::NAME}/file.md`
references; the actual home prefix lives only in the path-atom file's
frontmatter, registered in the local kei-registry.
NEW path atoms (`_blocks/path-*.md`):
- `path-user-memory.md` → template `~/.claude/memory`
- `path-user-rules.md` → template `~/.claude/rules`
Both files use frontmatter `type: atom, kind: path, template: ..., expand_at: render`.
BlockMdScanner auto-registers them; DNA index shows them under their
unprefixed names (`user-memory`, `user-rules`) for human lookup, while
the body sha8 makes them content-addressable.
Resolver (`_assembler/src/registry_client.rs`):
- `is_path_atom(conn, name)` — checks DB by name + filename convention
(`_blocks/path-<name>.md`) + frontmatter `kind: path`. Defensive:
filename + frontmatter must BOTH agree.
- `frontmatter_has_kind_path(body)` — minimal YAML parser. Tolerates
CRLF, quoted values, rejects substring matches (`pathological` ≠ `path`).
- 5 unit tests cover positive + 4 negative cases.
Resolver wire-up (`_assembler/src/assembler.rs:147 write_references`):
- For each `references.extra` entry starting with `path:NAME/...`:
- Lookup `NAME` via `is_path_atom`.
- On success: emit `{path::NAME}/<suffix>` — opaque, kit-resolvable.
- On miss: stderr warn + passthrough. Never fatal.
- Non-`path:` refs pass through unchanged. Backward compatible.
- 2 unit tests cover passthrough paths.
Manifest migration (38 manifests touched):
- `~/.claude/rules/<file>` → `path:user-rules/<file>`
- `~/.claude/memory/<file>` → `path:user-memory/<file>`
- 96 references migrated; 1 prose-style reference in security-auditor
left as plain text (lives inside a domain_in description, not in
references.extra — out of scope for this resolver).
Regenerated 38 `_generated/*.md` + 1 new `frontend-validator.md`.
Regenerated `docs/DNA-INDEX.md` (now includes 2 path-atoms by name).
Verification (cited):
- `git ls-files | grep denisparfionovich` → 0 hits outside allowlist
(NOTICE/README byline + `.github/workflows/leak-check.yml` detection
rule).
- `_generated/` contains 99 occurrences of `{path::user-...}/`.
- assembler tests: 29 passed (5 new). kei-registry tests: 10 passed
(8 short_path from earlier commit + 2 unrelated).
- assembler resolver verified end-to-end: ml-implementer.md line
479-485 shows `{path::user-rules}/ml-protocol.md` etc.
What this does NOT do (deferred):
- No registry-DB schema change. Path atoms ride existing Atom block-
type via convention, not via new `BlockType::PathAtom` variant.
- No git-branch tracking (Phase 2 of plan).
- No `kei-registry status` cross-cutting CLI (Phase 3 of plan).
- No path-atom orphan detection CLI (Phase 4).
The path:user-memory and path:user-rules cover 100% of the username-
leak surface from the current manifest set; future categories
(kit-root, registry-db, sync-repo, secrets-env, project-root) can
land additively without architectural changes.
=== STATUS-TRUTH MARKER ===
shipped: functional
stubs: 0
cargo-check: PASS
behaviour-verified: yes
follow-up-required:
- Phase 2 (git-branch tracker hook)
- Phase 3 (kei-registry status subcommand)
- Phase 4 (orphan detection CLI)
- Sync user-side install: ~/.claude/agents/_manifests/ still has
pre-migration absolute paths; will pick up new format on next
`install.sh --add` (out of scope for this commit).
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Parfii-bot