Louvain only ever found the reasoning chains (the graph is disconnected
by nature — every connected component became its own cluster) and
edge-orphans could never join anything. Clusters are now RELATED TOPICS:
propositions grouped by meaning.
- Embedder (src/server/embeddings.ts): in-process transformers.js v4
running EmbeddingGemma-300M q8 (MTEB 68.4, ~300MB one-time download),
MRL-truncated to 512d, "title: none | text:" prefix on 100% of inputs,
L2-normalized so cosine = dot. Model/dim mismatch voids the ledger
(full re-embed). Injected at the composition root — the agent layer
never imports the server layer (architecture law).
- Ledger (data/graph/embeddings.json): model + dim + vectors + the
persisted cluster partition. Reclustering runs at the END of every
embedding batch (post-merge hook, both front doors) — never per read
(the agglomerative pass is ~1.5s at 338 nodes).
- Clustering (src/core/semantic-clusters.ts): hand-rolled average-linkage
agglomerative over cosine (npm HDBSCAN is an abandoned alpha). Stragglers
stay singletons by default; attachStragglers is the all-in toggle.
Threshold 0.60 swept on the real graph: 26 topics, 74/90 edge-orphans
land in real topics, 10 stragglers.
- Consumers (snapshot, settle, namer, replay) read the persisted
partition — one cluster concept everywhere; core-survival label
matching unchanged (20/26 topics kept labels).
- Louvain retired: detectCommunities + graphology* deps deleted
(graphology-louvain had leaked into the client bundle since the
clusters wave); scripts/bench-graph.ts (dead FA2 bench) removed.
- scripts/embed-graph.ts: backfill/cold-start (338 nodes in 150s
including the one-time model download).
The layout now EVOLVES instead of reshuffling on every extraction. A pure
core module (src/core/layout.ts) warm-starts forceAtlas2 from the positions
ledger (data/graph/positions.json, read-modify-write like sources.json,
updatedAt stamp for future live-physics conflict handling), re-blends every
previously-positioned node toward its anchor each iteration (retention 0.85
- old placements stay recognizable, strong forces still win), seeds new
nodes near their positioned neighbors, and seeds orphans on the rim outside
the core so they read as unconnected knowledge.
- Port/store: GraphStore.readPositions/writePositions; snapshot carries
positions when the ledger exists (optional - fresh graphs unchanged).
- Extraction pipeline settles synchronously after every merge (chat and
notes paths), before usage persist - the next /api/graph fetch already
reflects new nodes.
- View: the ledger IS the layout; the local one-shot FA2 pass survives
only as a fallback when no ledger exists.
- scripts/replay-layout.ts: simulates organic growth by replaying the
current 338-node graph one imported file at a time (real import order,
edges activate when both endpoints exist). Real run: 338 positions in
0.3s, 90-degree-0 orphans collecting at mean r=338 vs connected r=194.
- Also restores the cluster region fills (hull background colors) that
6692b19 had removed on a misreading of "no glow".
Live-verified: fit zoom derives from the ledger bbox, pickAt aligns with
ledger positions at every probe, hover/click/detail-card work, 408/408
tests, typecheck/lint/build green.
Future live physics stays cheap by design: the same pure function is the
merge-time settler and the future client simulator; a pinned node is just
an anchor with full retention.
Core-survival labelings (vision section 1, DECIDED 2026-09-13):
ClusterLabeling records in a new append-only ledger
(data/graph/cluster-labels.jsonl), immutable, id = clu_ + sha256 of the
sorted core so re-naming races and re-runs dedupe at the store seam.
matchClusterLabelings (core/clusters.ts, pure): a community keeps a
record's label while at least half its core survives in it; both sides
single-successor (a split keeps one name; greedy by overlap, ties to
the newer record).
The namer (src/agent/subagents/cluster-namer.ts): ONE singular cheap LLM
call (new 'labeler' role, glm-flash/low) names every new/changed
community at once, given member names + statements (capped at 12
members per cluster). refreshClusterLabels runs POST-EXTRACTION
(user-decided) from both front doors, fire-and-forget — naming failure
never fails the run; refreshes serialize behind a chain so parallel
imports never mint duplicate labels. import-notes.ts awaits
clusterNamingSettled before exit.
Payload: GraphSnapshot.clusters (>= MIN_CLUSTER_SIZE 3) joins detection
with labelings at read time — claimed clusters carry the record's label
and id; unlabeled ones carry a member-hash id and null label. Detection
is deterministic so no memo in v1 (ms at current scale; revisit at
vault scale).
Tests (372/372): matcher half-rule/split/merge/greedy/tie cases; naming
end-to-end through importNotes (one call, one record, claim on
re-refresh), naming failure non-fatal; snapshot derivation with
labeling join; 11 test pipelines now pin an explicit labeler seam.
The same extractor→auditor→merger pipeline now runs over raw personal
notes in arbitrary formats (vision §1, DECIDED 2026-09-13):
- NotesSource records (data/graph/sources.json, deterministic id from
path hash → idempotent re-imports) play the chatId role in mappings,
checkpoints, and observation events; usage lands on the source record
(appendSourceUsage, idempotent per startedAt, kept across upserts).
- mergeFindings is chat-store-free: callers pass MergeSource
{messages, foldedAt} — sessions pass the chat record, notes pass
messages:null (no quiz-event rebuild; a deterministic rebuild needs
structured quiz tool parts).
- Second extractor prompt (NOTES_EXTRACTOR_INSTRUCTIONS) for general-
purpose extraction; understanding judges the AUTHOR's grasp. Auditor
wording input-agnostic. extract/audit share one generic runSubmitAgent.
- graphSnapshot.fileSources (srcId→filePath); notes sources render as
static path entries in the detail card (FileTextIcon, never a link).
- One shared pipeline instance (exported from chat-handler): same
single-flight registry, live status chips (label = file path), usage
accounting, and true abort for both front doors.
- Transport: POST /api/graph/import (multipart, 3-wide worker pool) +
Import notes… button in the graph view; scripts/import-notes.ts for
batch runs (concurrency 4).
- real-data-extraction/ gitignored (raw import sources never committed).
355/355 tests; typecheck, lint, build green.
Diagnosis (2026-09-11 user testing, minimal-effort GLM): sessions stuck on
'plan' forever. Two causes: (1) the three-phase view read the stored tree's
currentNodeId, which nothing ever writes post author-once (2026-09-03) — a
structural dead seam; (2) the teacher stochastically left quiz.nodeId
untagged, and done-by-quiz-result semantics would have falsely completed
nodes anyway.
The redesign (docs/probe-teach-split.md) abolishes derived occupancy in
favor of explicit events:
- Two agents over one transcript: createProberAgent (quiz without a
nodeId field, ask, probe_done) and createTeacherAgent (full toolset,
plan_init onward). The chat-handler construction branch keys on a
probe_done part in the transcript. MODELS.prober added.
- probe_done: server-side seam tool — carries the learner assessment
(strands + free-form edge read), refuses while a question is open or
the probe is already concluded, and queues a handoff steer through the
generalized wake pipeline (steers now dedupe by id, not jobId; job
finalization only for job steers). The teacher auto-wakes and authors
the plan; the learner sees the assessment via the probe-done card.
- phases: probe ends at a concluded probe_done, plan ends at a
successful plan_init — strictly sequential, no skipping, no legacy
compatibility (data wiped at the pivot per doctrine).
- Plan map = position, not completion: derivePlanStatuses reads only
tagged quiz CALLS (state/outcome feed nothing); current = latest
tagged node with consecutive duplicates collapsed, visited = earlier
distinct stays (a revisit stays in both — current wins at render).
PlanTree is structure-only; currentNodeId/doneNodeIds and the dead
mutation helpers are gone. No fallback current.
- Prompts split per agent (prompts/prober/, prompts/teacher/ over the
trimmed shared base); graph-context injection removed entirely
(shelved, docs/probe-teach-split.md §5); knowledge-graph context no
longer reaches either agent.
- Plan blocks are full-only snapshots at plan_init (neighborhood
machinery retired; the persistent DAG window is the future UI wave);
usage capture unchanged.
Gates: tsc clean, 294/294 tests (phases/plan-tree/plan-blocks/question-
tools rewritten to the new semantics; probe-done + handoff-wake tests
added), lint, build. Live GLM smoke PASS: prober concluded with an honest
assessment, teacher auto-woke, authored a 10-node plan with the block
attached, then tagged checks on slope-instinct → secant derived current/
visited exactly as designed; grading honest both ways (driver off-by-one
proved a wrong answer grades false).
Extraction is real spend and background work; the dock needs to see
and stop it. User decisions: persist all cost data (chat record),
per-stage usage granularity, and TRUE cancellation for abort.
USAGE CAPTURE (live + persisted):
- extraction.ts: per-call onStepFinish captures each billed step's
usage (SDK LanguageModelUsage -> CallUsage: input/output/cache
read+write/reasoning) into the registry's live per-stage usage
(extractor/auditor; the merger is deterministic — no model call).
- /api/graph/status runs now carry usage (model + steps per stage);
cost/context folds are the consumer's (core/prices.ts — nothing
stores dollars).
- ChatRecord.extractions: append-only per-run usage log (mirrors the
turns log): startedAt key, at, durationMs, merge stats when the
merger ran, stages. Persisted on success AND failure — a failed run
still spent money. Idempotent per startedAt; the list payload
(ChatSummary) never leaks it.
- EmissionStats moved to contracts/graph.ts (its contract home);
core/graph.ts re-exports for existing importers.
- Verified end-to-end against the real pipeline (backfill one chat):
per-step token counts, reasoning tokens, and the auditor's growing
prompt-cache reads captured and persisted.
TRUE ABORT (the dock's abort button, user decision):
- RunningExtraction owns one AbortController per run, shared across
phases; abortExtraction(chatId) fires it and returns whether a run
was aborted (idempotent no-op otherwise). The pending model call
receives the signal — the provider cancels the request, spend
stops. throwIfAborted() at phase boundaries ends runs aborted in
sync gaps.
- Abort is a deliberate stop, not a failure: same ledger discipline
(nothing merged, nothing checkpointed, partial usage persisted) but
the run reports zero emissions instead of throwing. Exported via
src/server/observability.ts for master's /api/activity/abort route.
- Tests: mid-run abort (hanging mock that rejects on the signal),
live-accumulation + persisted-record assertions, store-seam
idempotency, and the summary-payload leak guard.
The extractor's per-proposition understanding observations (named-word
scale: solid/shaky/accepted/...) were ledger data since the redesign,
with no surface. This exposes them at read time and shows each
session's note as a small chip on its session row in the node detail
card — the per-session confidence history the user asked for, one
observation per (node, chat), latest wins within a chat.
- GraphSnapshot.nodeObservations: nodeId -> chatId -> note, built in
graphSnapshot() from observation events (pure read-time join).
- Sessions list rows: link + observation chip.
- Session-relative judgments stay session-scoped: they render next to
their session, never as node state (the state model stays pending).
The five-class NodeStateClass (taught/known/missed/dont-know/candidate)
was transitional scaffelage from the 2026-09-02 redesign, deriving state
by latest-quiz-wins — exactly what the philosophy rejects: understanding
is inferred at read time from the real state model (still pending
ideation), never encoded as quiz-derived classes.
- contracts: NodeStateClass deleted; GraphSnapshot no longer carries
nodeStates (objective graph + sessions only).
- core: deriveNodeStates replaced by latestQuizOutcomes — the raw
event fact (nodeId -> latest quiz kind), consumed ONLY by the
teacher's graph-as-context selection, never by the home renderer.
- graph-context: hotspot selection re-keyed to outcomes — groups are
now 'Hotspots (last answer wrong or don-t-know) / Answered correctly /
Never probed'. Same diagnostic selection, no state taxonomy.
- graph-view: nodes render uniformly (accent color, size 8); the panel
is search-only; the detail card's state badge is gone. Quiz outcomes
remain ledger data for the future state model.
Verified live (headless): uniform discs (single color/size, zero state
pixels), search-only panel, card = name + statement + sessions, no
console errors.
With real extracted data, full-sentence statements as canvas labels proved
unworkable: 10-line label blocks, illegible overprint clusters, bottom-edge
clipping. Per the user's 2026-09-08 decision:
- GraphNode/ExtractedProposition gain `name` — a very short, glanceable
label (glossary-headword style: "Will to power"), presentational only:
not unique, not identity, never precise. Set at creation; link-appends
never change it (first line defines; labels stay stable across sessions).
- `statement` keeps its full precision and becomes the identity anchor;
the detail card shows it under the name. `description` is dropped.
- Extractor coins the name (freshest session context); auditor carries it
through on create, rewording only clearly unglanceable names; linked
propositions keep the existing node's name.
- Renderer: canvas label = name; search matches name + statement;
detail card = name (bold) + statement (muted).
- Store guard requires name (pre-pivot node lines are skipped as legacy);
vision.md node-schema bullet + amendments table updated (2026-09-08).
The minimal implementation of the 2026-09-02 graph vision (docs/vision.md §1):
- contracts/graph.ts: every node is a TRUE proposition (statement is both
rendering label and identity key; required description; no kind, no name).
Edges are follows (derivable) / supports (grounds without entailing) with
message-granular provenance points {chatId, messageId}. Events reduce to
correct/miss/dont-know plus observation (understanding notes); no taught
events, no misconception kind.
- extraction.ts: extractor is TREE-BLIND (transcript only, no plan tree) and
free-form; auditor sees findings + the current graph, owns faithfulness and
identity (link-or-create verdict per proposition, recorded as linkTo);
transcriptView tags every line with its message id (provenance anchors).
- core/graph.ts merger: applies verdicts deterministically — linkTo appends
a link line (phrasings join aliases, provenance unions; reads merge by id),
absent creates; NO string matching anywhere. Quiz events rebuilt from tool
parts with attribution-only nodeId resolution; understanding notes become
observation events (obs:<sourceId>); mapping lines are the verdict audit
trail and make re-merges idempotent.
- deriveNodeStates: transitional — latest quiz event wins (known/missed/
dont-know, else candidate); taught unreachable until the state-model
ideation lands.
- graph-context.ts + 50-graph-context.md: follows chains, hotspot grouping,
state vocabulary updated for the new event kinds.
- graph-view.tsx: node label is the statement; detail shows statement +
description.
- tests: merger verdicts (link, no-string-match, cross-chat assertions),
tree-blind pipeline end-to-end, follows vocabulary in context tests.
276/276 green.
Schema: GraphNode + ExtractedProposition carry 'name' — a short 2-6 word
header, the rendering handle. Node theory made explicit: a node is an
objective world-facing fact; the learner's relationship to it lives
entirely in the event ledger (state labels are derived, never stored).
Extractor + auditor instructions enforce it — misconceptions state the
wrong idea itself as a claim, never 'the learner believes Y'. Legacy
ledger lines without a name derive one from the statement on read.
graph-view: labels use the name; the detail panel shows name as header
and statement as body.
The knowledge graph's write channel is now the pivot's target
architecture (vision §1 construction):
- src/agent/subagents/extraction.ts — the pipeline factory
(createExtractionPipeline({ chatStore, graphStore, extractor?,
auditor? }); models env LH_EXTRACT_MODEL ?? LH_MODEL):
* transcriptView(): the compact view both LLM stages see — final plan
tree with node ids, conversation verbatim, QUIZ lines with outcomes,
mark_done lines; job tool parts are one-liners, plan ops fold into
the tree line.
* Extractor: transcript → SessionFindings (propositions incl.
misconceptions and prose-only supports edges, attribution for
UNTAGGED probes, all with verbatim evidence) via one zod-validated
submit_findings call.
* Auditor: transcript + findings → the verified subset + drops (the
faithfulness net) via submit_review.
- src/core/graph.ts — emitChat/foldStaleChats/replayFinalTree retire;
mergeFindings() replaces them as the pipeline's deterministic apply
stage: exact/alias identity resolution (one mapping line per (chat,
graph node)), edge dedupe, and event rebuild FROM THE TRANSCRIPT's tool
parts — kinds/timestamps/refs/notes deterministic, the LLM's only event
say being WHICH proposition an untagged probe tested (retroactive —
the vision's open question #3, resolved structurally: tagged events
resolve deterministically; attribution rescues untagged and
tagged-but-unmapped ones; unattributable land null + question text).
pendingQuizAnswers() is the trigger helper.
- Trigger (turn-service.ts triggerExtraction, replacing the old
foldTurnIntoGraph body): once a chat accumulates
EXTRACTION.everyNQuizAnswers (LH_EXTRACT_N, default 3) new answered
quizzes, fire the pipeline async — single-flight per chat, failure
checkpoints nothing and re-runs on the next trigger. Deliberately a v1
placeholder isolated in ONE seam, trigger-agnostic pipeline.
- GET /api/graph is now a pure read (foldStaleChats gone).
- NodeMapping.treeNodeId → sourceId (the mapping key is now the writer's
local proposition id — tree node when tree-derived); store strict-read
schema updated. Local ledger data regenerates through the pipeline.
- Tests: graph.test.ts rewritten around mergeFindings (identity,
attribution paths incl. ghost-rescue, idempotency, cross-session
provenance, trigger counting), graph-context.test.ts merge section
converted to findings-driven, NEW extraction.test.ts — transcriptView
units + the full pipeline with mock models (audit drops, failure
checkpoints nothing, single-flight). 195/195, tsc/eslint/build clean.
Probe attribution (vision open question): probes attach retroactively by
the extractor against the whole transcript; a pre-tree probe maps to a
proposition the tree only articulates later. Fuzzy/embedding merge
adjudication stays deferred (conservative exact/alias only).
Per-entity semantic ports (src/core/ports.ts), one adapter family
(src/store/*, fs JSON/JSONL), exactly one composition point
(src/server/stores.ts). Dependency direction is now machine-checked:
adapters implement core interfaces; core never imports an adapter.
The inversion:
- core/graph.ts (emitChat/getGraph/graphSnapshot/foldStaleChats) is now
pure — it takes the storage ports as explicit parameters (GraphDeps).
No store imports; newGraphNodeId is local; node id format unchanged.
- core/graph-context.ts buildGraphContext() no longer defaults to the
live ledgers: the chat-handler hands in getGraph(graphStore) per turn.
- store adapters export exactly one object each implementing their port
(chatStore/graphStore/jobStore); bodies otherwise verbatim.
NodeMapping + SessionCheckpoint moved store/graph -> core/contracts
(they ARE contract shapes); CreateJobInit/JobPatch live in ports.
- titleFromPrompt moved store/chats -> core/contracts (pure helper,
planNodeStatus precedent). Store modules now contain persistence only.
- server/stores.ts is the composition root; server/{chats,graph,jobs}.ts
and chat-handler wire from it; agent (plan tools, sub-agent runner)
call the port objects. The shell surface (@/src/server exports) is
unchanged.
Lint law extended: the whole of src/core is now a purity zone (was a
file glob with a graph/graph-context exemption). Verified it fires on
core->store imports; tsc clean, 190/190 tests, eslint clean, prod build
clean (prerender 6/6). Tests pass deps explicitly — graph.test uses the
same fs-adapter pair stores.ts wires in production; graph-context.test
keeps its in-memory ledgers as a GraphStore implementation.
The shell now imports through exactly two barrels, enforced by
import/no-restricted-paths (npm run lint):
components/** -> "@/src/core" (pure core API, browser-safe)
app/** -> "@/src/core" + "@/src/server" (server entries)
Zone violations are lint errors with architecture-pointer messages; the
pure-core modules (contracts, question-core, plan-tree, phases, pending,
math-delims, ui-message) may never import agent/server/store.
Supporting moves (direction: IO layers -> core):
- core/index.ts: the core public API barrel
- core/ui-message.ts: moved from src/agent (it was shell-facing all along)
- quiz/ask input zod schemas moved agent/tools -> core/question-core
(the question contract, alongside the grading logic)
- ChatRecord/ChatSummary moved store/chats -> core/contracts (single schema)
- GraphSnapshot/NodeStateClass moved core/graph -> core/contracts (the
/api/graph payload IS a contract; the pure renderer needs only these)
- src/server/{chats,graph,jobs}.ts + index.ts: thin server entries for the
transport layer; GET /api/graph's fold side-effect now lives behind
graphView() instead of inline in the route
Gates: tsc clean, 190/190 tests, eslint clean (law verified to fire on
store/agent/subpath violations), production build clean.
(Repo repair en route: a git object (app/chat/[id] tree) was missing from
the object store — reconstructed byte-exactly via mktree from its blob;
the broken node_modules that stalled the build was cleanly reinstalled.)
amosblomqvist