arborist/docs/diagrams
russell@unturf.com de07ad9392
docs: distill #000008+#000009+#000010 into core docs + diagrams
Three Explore agents fanned out in parallel for a docs/ + diagrams/
+ code-comment audit against the shipped state of the three
preflight tickets. This commit lands all the alignment fixes.

Core docs updates:

  CLAUDE.md
    - dag.py module description: stage counts now read
      "7/8 quote · 9/10 CTI · 3 reject" reflecting #000009 preflight
      stage + reject-broad early-return shape.

  docs/cti-architecture.md §2.2 + §2.3
    - §2.3 Merkle-AGI-DAG section rewritten: documents all five DAG
      shapes (legacy 7/9, post-#000009 8/10, reject-broad 3),
      describes the preflight stage's 5 nested CTI clauses
      (classifier / answer_contract / prompt_contract /
      evidence_contract / policy_refs), pins
      PREFLIGHT_NODE_VERSION = "preflight-node-v1", states the
      audit-replay payoff.
    - §2.2 CTI section: adds the four new modules
      (quantifier, model_profiles, quantifier_reminder,
      metacognition) as code anchors. Notes that pre-answer
      preflight contract extends CTI upstream of retrieval.

  docs/seven-point-program.md
    - D3 status ½ → ¾ — pre-answer preflight contract landed via
      #000008 + #000010. Code anchors + pinning tests updated.
    - D4 status ½ → ¾ — preflight stage adds upstream control
      commitment to the run-DAG. Code anchors include
      build_reject_run_dag + preflight_node_hash.
    - Status snapshot table: tickets column now references
      #000008/#000009/#000010 against D1/D3/D4 directives.
    - "Post-landing addendum (2026-05-03 / 2026-05-04)" subsection
      summarises all three tickets + their commit shas + final
      test count (993 passing, up from 734).

  docs/modules.md
    - Q&A pipeline table: added 4 new modules (quantifier.py,
      model_profiles.py, quantifier_reminder.py, metacognition.py).
      dag.py row updated to "7/8 quote · 9/10 CTI · 3 reject".
    - dag.py subsection rewritten: documents all 5 DAG shapes,
      describes the preflight payload's 5 clauses + question_state.
    - 4 new module subsections (quantifier / model_profiles /
      quantifier_reminder / metacognition) explaining each
      module's purpose, signature, and how it feeds the run-DAG
      preflight clause.

Diagram updates:

  docs/diagrams/query-pipeline.dot + .svg
    - New "PREFLIGHT (#000008 + #000010)" node inserted between
      cache_check and concepts_lookup.
    - New "REJECT-BROAD" node showing the 3-stage minimal DAG
      escape path.
    - render node label extended with the audit-line tail token
      catalog.

  docs/diagrams/aborist-modules.dot + .svg
    - 4 new qa_* nodes in the retrieval & verifier cluster.
    - 8 new edges: qa_query/qa_runner each call into all 4
      preflight modules; qa_dag has dotted edges to qa_quantifier
      + qa_metacognition (preflight clause sources).
    - qa_dag label updated to mention preflight_node_hash + 5 clauses.

  docs/diagrams/verifier-ladder.dot + .svg
    - Soft-demote violations list extended: BROAD_QUANTIFIER_RUNAWAY
      / CAP_APPLIED / SCOPE_UNBOUND, FORMAT_COLLAPSED, BARE_NAME_CLAIM.
    - New "AUDIT-LINE TAILS" annotation node listing all 11 tail
      tokens (#000008 broad-* + #000010 metacog + classic verifier).
    - Dashed edges from each rung to tails note showing tails
      compose onto labels.

Code-side stale-comment fixes (caught by 3rd Explore agent):

  aborist/qa/keys.py:218
    - "The four fields" → "The seven fields"; mention #000010 adds
      six more for metacognition.
  aborist/qa/query.py:2644
    - 7-stage / 9-stage comment expanded to enumerate all four
      base+preflight shapes plus the 3-stage reject path.
  aborist/qa/runner.py:835
    - same expansion as query.py for runner.ask() callsite.

mesh-*.dot, ingest-pipeline.dot, qa-modes-bench.md, bench-maxing.md,
bench-emergent-design.md, verifier-semantic-gap-design.md,
self-reference-design.md, concept-relations-design.md confirmed
orthogonal — no edits needed.

993 tests still passing (no behavior change). 7 files modified
across docs/ + 3 dot diagrams + 3 SVGs + 4 code-comment fixes.
2026-05-03 19:18:22 -04:00
..
aborist-modules.dot docs: distill #000008+#000009+#000010 into core docs + diagrams 2026-05-03 19:18:22 -04:00
aborist-modules.png docs: README label refresh + per-module reference + Graphviz diagrams 2026-05-01 23:19:01 -04:00
aborist-modules.svg docs: distill #000008+#000009+#000010 into core docs + diagrams 2026-05-03 19:18:22 -04:00
ingest-pipeline.dot docs: README label refresh + per-module reference + Graphviz diagrams 2026-05-01 23:19:01 -04:00
ingest-pipeline.png docs: README label refresh + per-module reference + Graphviz diagrams 2026-05-01 23:19:01 -04:00
ingest-pipeline.svg docs: README label refresh + per-module reference + Graphviz diagrams 2026-05-01 23:19:01 -04:00
mesh-data-flow.dot docs: mesh multiplayer protocol with dot diagrams 2026-04-28 12:54:36 -04:00
mesh-data-flow.png docs: mesh multiplayer protocol with dot diagrams 2026-04-28 12:54:36 -04:00
mesh-data-flow.svg docs: README label refresh + per-module reference + Graphviz diagrams 2026-05-01 23:19:01 -04:00
mesh-epoch-lifecycle.dot docs: mesh multiplayer protocol with dot diagrams 2026-04-28 12:54:36 -04:00
mesh-epoch-lifecycle.png docs: mesh multiplayer protocol with dot diagrams 2026-04-28 12:54:36 -04:00
mesh-epoch-lifecycle.svg docs: README label refresh + per-module reference + Graphviz diagrams 2026-05-01 23:19:01 -04:00
mesh-group-decisions.dot docs: mesh multiplayer protocol with dot diagrams 2026-04-28 12:54:36 -04:00
mesh-group-decisions.png docs: mesh multiplayer protocol with dot diagrams 2026-04-28 12:54:36 -04:00
mesh-group-decisions.svg docs: README label refresh + per-module reference + Graphviz diagrams 2026-05-01 23:19:01 -04:00
mesh-identity-stack.dot docs: mesh multiplayer protocol with dot diagrams 2026-04-28 12:54:36 -04:00
mesh-identity-stack.png docs: mesh multiplayer protocol with dot diagrams 2026-04-28 12:54:36 -04:00
mesh-identity-stack.svg docs: README label refresh + per-module reference + Graphviz diagrams 2026-05-01 23:19:01 -04:00
mesh-secret-envelope.dot docs: mesh multiplayer protocol with dot diagrams 2026-04-28 12:54:36 -04:00
mesh-secret-envelope.png docs: mesh multiplayer protocol with dot diagrams 2026-04-28 12:54:36 -04:00
mesh-secret-envelope.svg docs: README label refresh + per-module reference + Graphviz diagrams 2026-05-01 23:19:01 -04:00
query-pipeline.dot docs: distill #000008+#000009+#000010 into core docs + diagrams 2026-05-03 19:18:22 -04:00
query-pipeline.png docs: README label refresh + per-module reference + Graphviz diagrams 2026-05-01 23:19:01 -04:00
query-pipeline.svg docs: distill #000008+#000009+#000010 into core docs + diagrams 2026-05-03 19:18:22 -04:00
verifier-ladder.dot docs: distill #000008+#000009+#000010 into core docs + diagrams 2026-05-03 19:18:22 -04:00
verifier-ladder.png docs: README label refresh + per-module reference + Graphviz diagrams 2026-05-01 23:19:01 -04:00
verifier-ladder.svg docs: distill #000008+#000009+#000010 into core docs + diagrams 2026-05-03 19:18:22 -04:00