FE-808 persist graph node ordinals

[lunelson]

FE-808 persist graph node ordinals

FE-808 normalize graph approval basis

FE-808 resolve graph references by code

FE-808 enforce supersession acyclicity

FE-808 split active graph projection

Align probe transcripts with Pi context rendering

Amp-Thread-ID: https://ampcode.com/threads/T-019e92bc-e43a-727f-8acf-0213915029ff
Co-authored-by: Amp amp@ampcode.com

FE-808 canonicalize graph tool handles

Stub projection and format topology for LLM context

Amp-Thread-ID: https://ampcode.com/threads/T-019e92bc-e43a-727f-8acf-0213915029ff
Co-authored-by: Amp amp@ampcode.com

Thread representative LLM projection seams

Amp-Thread-ID: https://ampcode.com/threads/T-019e92bc-e43a-727f-8acf-0213915029ff
Co-authored-by: Amp amp@ampcode.com

Apply remaining context rendering cleanup

Amp-Thread-ID: https://ampcode.com/threads/T-019e92bc-e43a-727f-8acf-0213915029ff
Co-authored-by: Amp amp@ampcode.com

FE-808: Normalize graph tool outcomes

FE-808: Add existing-code graph probe

FE-808: Add retry diagnostics graph probe

FE-808: Add ambiguity no-overcommit probe

FE-808: Close graph commit planner judo findings

Add fixture seed loader and consolidate Bilal-port seed fixtures

Restructure .fixtures/seed-specs/ into .fixtures/seeds/bilal-port/ with
vendored Bilal originals under _originals/, the throwaway port script, and
one consolidated .json per spec ({spec, nodes, edges}).

Fix the port script's basis mapping: epistemicStatus no longer maps to the
invalid 'accepted_review_set' basis (forbidden per GRAPH_MODEL.md). Bilal
authored each item directly, so every ported node is 'explicit'; the
epistemic flavor is preserved in source text instead.

Add src/graph/seed-fixtures.ts: a loader that commits each consolidated
fixture through CommandExecutor (createSpec + one explicit commitGraph
batch) so graph clock / change log / lsn stay coherent. Lives in graph/
(not db/) to respect the db/ <- graph/ dependency direction. Exposed via
'npm run seed'; covered by src/graph/seed-fixtures.test.ts.

Amp-Thread-ID: https://ampcode.com/threads/T-019e91ee-aa39-73d2-a346-a0ae1e55e3b9
Co-authored-by: Amp amp@ampcode.com

Self-validate ported seeds against the real loader before writing

The port script now runs each assembled seed through seedFixture against a
throwaway in-memory DB before writing .json, reusing the exact
structural validation commitGraph enforces (planCommitGraph: node
kind/plane/detail + edge category/stance/ref/cycle checks). A seed that
would not commit cleanly aborts the run instead of producing an unloadable
fixture.

Amp-Thread-ID: https://ampcode.com/threads/T-019e91ee-aa39-73d2-a346-a0ae1e55e3b9
Co-authored-by: Amp amp@ampcode.com

plan: add dev-seed-fixtures parallel frontier

Capture the landed seed-fixture substrate (consolidated {spec,nodes,edges}
contract, src/graph/seed-fixtures.ts loader, npm run seed, self-validating
port scripts) and the two enhancement ideas as backlog: (1) enrich
Bilal-port graphs through Brunch from the original briefs to recover
thesis/goal structure, (2) port + enhance the legacy product fixtures.
Notes manual-testing.md seed-doc drift for the doc-reconciliation track.

Amp-Thread-ID: https://ampcode.com/threads/T-019e91ee-aa39-73d2-a346-a0ae1e55e3b9
Co-authored-by: Amp amp@ampcode.com

FE-808 validate createNode basis

agent and skill guidance re not deleting stubs

FE-808: Sync graph resilience closeout

[lunelson]

Warning

This pull request is not mergeable via GitHub because a downstack PR is open. Once all requirements are satisfied, merge this PR as a stack on Graphite.
Learn more

• FE-808 persist graph node ordinals #171 👈 (View in Graphite)
• Sync plan for FE-806 start #169
• FE-795: Track live graph observer frontier #166
• FE-785: M5 agent-graph-integration #163
• FE-776: Graph Layer preps #162
• FE-744: Document Pi command containment evidence #150
• FE-737: Web shell over the same host (M3) #147
• FE-736: JSONL session viability proof (M2) #146
• FE-735: Mode shell and fixture driver (M1) #144
• FE-702: Walking skeleton — brunch binary + TUI over pi (M0) #142
• next

This stack of pull requests is managed by Graphite. Learn more about stacking.

[cursor]

PR Summary

Low Risk
Changes are agent-skill guidance and committed probe/seed fixture artifacts; no runtime graph or auth paths in this diff slice.

Overview
Adds deletion guardrails across ln-build, ln-review, ln-judo-review, and earned-mode ln-plan: comment-rich export {} files must be treated as intentional topology stubs per AGENTS.md §intentional topology stubs—build/cleanup, review delete findings, and delete-as-progress / judo deletions need explicit proof the documented seam is obsolete or absorbed, not merely unused.

Checks in three A14-L propose-graph-commit probe runs under .fixtures/runs/propose-graph-commit/ (existing projected-code edge via {existingCode: "G1"}, STRUCTURAL_ILLEGAL then corrected retry, ambiguous user prompt with clarification and no commit_graph), each with report.json, session.jsonl, and transcript.md.

Removes the legacy split fixture .fixtures/seed-specs/bilal-port/code-health/edges.json in favor of the consolidated Bilal-port seed shape described elsewhere in the branch.

^{Reviewed by Cursor Bugbot for commit 03a8137. Bugbot is set up for automated code reviews on this repo. Configure here.}

[Copilot]

Pull request overview

This PR advances FE-808’s “graph write contract” by persisting per-kind node ordinals (projected node codes), normalizing graph approval basis to explicit|implicit, tightening supersession/active-context projections, and aligning probe transcripts with Pi-derived LLM-visible context. It also adds a dev seed-fixture substrate (npm run seed) that loads consolidated fixtures through the CommandExecutor mutation boundary.

Changes:

• Persist nodes.kind_ordinal with per-(spec, plane, kind) monotonic allocation (node_kind_counters), expose projected node codes, and add selected-spec code → node id resolution.
• Normalize graph basis semantics (explicit|implicit), retire accepted_review_set, and route tool/adapter paths through projected codes (no raw node ids in agent tools).
• Introduce transcript projection + formatting modules and add a seed-fixture loader + tests, plus probe/report updates.

Reviewed changes

Copilot reviewed 104 out of 119 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
src/structured-exchange/project/request-review.ts	Add intentional projection seam stub.
src/structured-exchange/project/request-choices.ts	Add intentional projection seam stub.
src/structured-exchange/project/request-choice.ts	Add intentional projection seam stub.
src/structured-exchange/project/request-answer.ts	Add intentional projection seam stub.
src/structured-exchange/project/present-review-set.ts	Add intentional projection seam stub.
src/structured-exchange/project/present-question.ts	Implement canonical projection for present_question.
src/structured-exchange/project/present-options.ts	Add intentional projection seam stub.
src/structured-exchange/project/present-candidates.ts	Add intentional projection seam stub.
src/structured-exchange/project/capture-review.ts	Add intentional projection seam stub.
src/structured-exchange/project/capture-choices.ts	Add intentional projection seam stub.
src/structured-exchange/project/capture-choice.ts	Add intentional projection seam stub.
src/structured-exchange/project/capture-candidate.ts	Add intentional projection seam stub.
src/structured-exchange/project/capture-answer.ts	Add intentional projection seam stub.
src/structured-exchange/format/request-review.ts	Add intentional formatting seam stub.
src/structured-exchange/format/request-choices.ts	Add intentional formatting seam stub.
src/structured-exchange/format/request-choice.ts	Add intentional formatting seam stub.
src/structured-exchange/format/request-answer.ts	Add intentional formatting seam stub.
src/structured-exchange/format/present-review-set.ts	Add intentional formatting seam stub.
src/structured-exchange/format/present-question.ts	Implement markdown formatting for projected present_question.
src/structured-exchange/format/present-options.ts	Add intentional formatting seam stub.
src/structured-exchange/format/present-candidates.ts	Add intentional formatting seam stub.
src/structured-exchange/format/capture-review.ts	Add intentional formatting seam stub.
src/structured-exchange/format/capture-choices.ts	Add intentional formatting seam stub.
src/structured-exchange/format/capture-choice.ts	Add intentional formatting seam stub.
src/structured-exchange/format/capture-candidate.ts	Add intentional formatting seam stub.
src/structured-exchange/format/capture-answer.ts	Add intentional formatting seam stub.
src/session/session-transcript.ts	Replace bespoke transcript rendering with projection+formatter pipeline.
src/session/session-transcript.test.ts	Update transcript expectations to Pi-derived projection/markdown rendering.
src/session/project/transcript-context.ts	New Pi-derived transcript projection (filter to markdown-bearing content).
src/session/format/transcript.ts	New transcript markdown formatter.
src/rpc/handlers.test.ts	Update tests for commitGraph created-node result shape.
src/render/toon.ts	Add intentional TOON formatting substrate stub.
src/render/markdown.ts	Add shared markdown helpers for formatters.
src/probes/public-rpc-parity-proof.test.ts	Update transcript assertions to new tool-result headings.
src/probes/propose-graph-commit-proof.test.ts	Expand proof scenarios + adapt to created-node/code evidence.
src/graph/workspace-store.ts	Add selected-spec resolveNodeCode reader.
src/graph/spec-ownership.test.ts	Update node-id assertions + strengthen tool-schema specId guard checks.
src/graph/snapshot.ts	Add graph projections, node code resolver, kindOrdinal mapping, edge filtering.
src/graph/snapshot.test.ts	Extend tests for code metadata, kindOrdinal, active vs truth projections.
src/graph/seed-fixtures.ts	New consolidated seed-fixture loader + CLI (npm run seed).
src/graph/seed-fixtures.test.ts	New tests proving loader runs through command boundary and preserves clock/log.
src/graph/schema/nodes.ts	Add kind metadata, projected-code parse/format, and kindOrdinal on GraphNode.
src/graph/schema/edges.ts	Update basis semantics comment for `explicit
src/graph/README.md	Update topology/docs for new commitGraph planner and code/ordinal contract.
src/graph/project/reconciliation-needs.ts	Add intentional projection seam stub.
src/graph/project/overview.ts	Add intentional projection seam stub.
src/graph/project/neighborhood.ts	Implement neighborhood projection using projected codes.
src/graph/project/commit-result.ts	Add intentional projection seam stub.
src/graph/index.ts	Re-export projected-code helpers and new overview option types.
src/graph/format/reconciliation-needs.ts	Add intentional formatter seam stub.
src/graph/format/overview.ts	Add intentional formatter seam stub.
src/graph/format/neighborhood.ts	Implement neighborhood formatting for projected neighborhood.
src/graph/format/commit-result.ts	Add intentional formatter seam stub.
src/graph/command-executor/commit-graph-types.ts	New commitGraph input/result types (created node identity includes code).
src/graph/command-executor/commit-graph-batch.ts	New shared batch planner (validation, supersession cycle detection).
src/db/schema.ts	Persist kind_ordinal, add unique index, add node_kind_counters, update bases.
src/db/row-schemas.ts	Add typebox schemas for node_kind_counters.
src/db/README.md	Document new ordinal/counter storage contract.
src/brunch-tui.ts	Thread resolveNodeCode into runtime snapshots.
src/agents/contexts/node.ts	Switch node context rendering to projected neighborhood formatter.
src/agents/contexts/node.test.ts	Update expectations to projected codes in node context.
src/agents/contexts/graph.ts	Render graph context nodes/edges using projected codes.
src/agents/contexts/graph.test.ts	Add kindOrdinal in graph context fixtures.
src/.pi/extensions/structured-exchange/present-question.ts	Route tool through project + format seam for durable details/content.
src/.pi/extensions/graph/tool-schemas.ts	Update tool schemas to use projected codes (existingCode, nodeCode).
src/.pi/extensions/graph/review-set-proposal.ts	Make review-set translation basis: 'explicit' and remove per-item basis.
src/.pi/extensions/graph/index.ts	Resolve node codes in adapters; return STRUCTURAL_ILLEGAL (no throws) for bad codes.
src/.pi/extensions/graph/command-adapter.ts	Resolve existingCode → node id, format created nodes by code, export diagnostics formatter.
src/.pi/tests/structured-exchange-present-request.test.ts	Add test proving present_question uses shared project+format seam.
src/.pi/tests/review-set-proposal.test.ts	Assert review-set commits are explicit and don’t leak per-item basis fields.
src/.pi/tests/prompting.test.ts	Update prompt context fixtures for kindOrdinal + snapshots API addition.
src/.pi/tests/graph-tools.test.ts	Update schemas + adapters tests for projected codes and created-node result shape.
package.json	Add npm run seed.
memory/SPEC.md	Update FE-808 evidence claims and test coverage references.
memory/PLAN.md	Mark FE-808 done; add dev seed-fixtures frontier; archive notes.
memory/cards/graph-tool-resilience--graph-write-contract.md	Delete completed scope card.
drizzle/meta/_journal.json	Record new migration.
drizzle/0001_aspiring_orphan.sql	Add node_kind_counters + nodes.kind_ordinal + unique indexes.
docs/archive/PLAN_HISTORY.md	Archive FE-808 closeout notes.
docs/architecture/probes-and-transcripts.md	Update transcript.md description.
AGENTS.md	Document “intentional topology stubs” convention.
.fixtures/seeds/bilal-port/README.md	Update seed fixture location and consolidated contract docs.
.fixtures/seeds/bilal-port/_port-script.ts	Update port script to consolidated contract + self-validation through loader.
.fixtures/runs/propose-graph-commit/2026-06-04-retry-diagnostics/transcript.md	Add new probe transcript artifact.
.fixtures/runs/propose-graph-commit/2026-06-04-retry-diagnostics/session.jsonl	Add new probe session artifact.
.fixtures/runs/propose-graph-commit/2026-06-04-retry-diagnostics/report.json	Add new probe report artifact.
.fixtures/runs/propose-graph-commit/2026-06-04-existing-code-ref/transcript.md	Add new probe transcript artifact.
.fixtures/runs/propose-graph-commit/2026-06-04-existing-code-ref/session.jsonl	Add new probe session artifact.
.fixtures/runs/propose-graph-commit/2026-06-04-existing-code-ref/report.json	Add new probe report artifact.
.fixtures/runs/propose-graph-commit/2026-06-04-ambiguity-no-overcommit/transcript.md	Add new probe transcript artifact.
.fixtures/runs/propose-graph-commit/2026-06-04-ambiguity-no-overcommit/session.jsonl	Add new probe session artifact.
.fixtures/runs/propose-graph-commit/2026-06-04-ambiguity-no-overcommit/report.json	Add new probe report artifact.
.agents/skills/ln-review/SKILL.md	Add deletion-guard guidance for intentional topology stubs.
.agents/skills/ln-plan/references/earned.md	Add deletion-guard guidance for intentional topology stubs.
.agents/skills/ln-judo-review/SKILL.md	Add deletion-guard guidance for intentional topology stubs.
.agents/skills/ln-build/SKILL.md	Add deletion-guard guidance for intentional topology stubs.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.