af666aaa3f5449f08e009f9a620905d7264f0a62
10
Commits
| Author | SHA1 | Message | Date | |
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 amosblomqvist
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af666aaa3f |
physics: bundles join their cluster; depth runs over the logical graph
Owner-approved brief (orchestrator, physics arc): two laws.
1. IMP-NODE CLUSTER ASSIGNMENT. Imp nodes were unclustered (the partition
runs over stored propositions only) — no centroid pull, outside the
painted hulls, bundles sitting on the periphery pointing outward.
Now: a derived imp node's cluster is a function of its derivation —
MAJORITY among its PREMISES' birth sessions (owner: premises, NOT the
conclusion), ties to the chain's OWN birth (its provenance's first
point — the asserting session; deterministic, coincides with the
unanimous common case). Imp nodes are always re-derived, never
birthed, so the assignment must be exactly this.
Seam chosen: core/session-clusters.ts exports impClusterKey + a
shared attachImpToCommunities that mutates a communities list's
members IN PLACE. graphSnapshot attaches AFTER the hull filter (a
2-proposition community + its bundle never resurrects a hull — the
filter counts propositions); settleGraphLayout attaches to the
unfiltered partition (settle pulls every community; hulls are a
canvas-only concern). Both cluster-membership consumers — the sim's
centroid pull and buildRegions' rasterization — read it through the
members lists that went through the one helper, so the resting
ledger and the live sim agree on where bundles belong.
2. DEPTHS OVER THE LOGICAL GRAPH. inferenceDepths ran Tarjan over the
DRAWN edges (premise→imp→conclusion), inflating every multi-premise
conclusion one hop (depth(imp)+1 instead of depth(premises)+1) and
ranking the geometry point itself. Now:
- deriveView additionally emits logicalEdges — every chain contracted
to direct premise→conclusion arrows over PROPOSITION ids only
(per-premise, deduped — a conclusion's rank is max over premises,
which a single arbitrary premise edge could not express).
- GraphSnapshot carries logicalEdges; createGraphSimulation /
incrementalLayout accept a logicalEdges option: the depth
machinery (orphan detection AND the rank pass) reads it, springs
keep the drawn edges. Absent = edges (legacy behavior).
- Imp nodes join the ORPHAN-EXEMPTION mask explicitly — never pinned
to a level, keep the full regular forces (gravity, cluster pull,
springs), settle naturally between premise and conclusion levels;
the rank map is computed over propositions only, so arg_ ids are
absent from it by construction.
Wiring: settle + canvas (CanvasData.logicalEdges → buildSim) +
replay-layout all pass the logical set.
EXTRA FIX (in-slice discovery, one line, graph-server domain):
server/graph.ts graphClusters — the practice picker's /api/graph/
clusters — partitioned snap.NODES (the canvas image, imp nodes riding
it since chains-primary), leaking arg_ ids into nodeIds: pickable ids
that silently vanish inside chainsForSelection while nodeCount lied.
Now partitions snap.propositions — same purity law as the chain
table's 767a559 fix.
Tests (+13): impClusterKey pins (unanimous; cross-session majority; tie
→ chain's own birth, not the conclusion's); attach pins (members gain
the imp id, sorted; single-premise attaches nothing — no node exists;
dangling mints nothing; home absent from the list stays unattached);
snapshot pins (imp id rides cluster members to both consumers; the hull
filter counts propositions); logical-depth pins (multi-premise
conclusion at premises'+1 NOT +2; imp absent from the rank map);
depth-force exemption pin (rows pin crisply, arg_x floats unpinned —
old behavior stamped it onto the conclusion's row); deriveView logical
arrows (per-premise, deduped, proposition ids only).
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amosblomqvist
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4985b6f9fa |
chains-primary: stored chains replace typed edges; edges become a derived view
Owner rulings 2026-09-30: reasoning chains are the stored truth; the graph canvas renders a lossy derived image. No migration, no backcompat — old graph data was wiped. - contracts: GraphChain (arg_-minted id, premises, conclusion) replaces typed edges; GraphEdge survives only as the untyped derived arrow; GraphSnapshot carries stored chains; supports edges retired entirely - store: chains.jsonl ledger (edges.jsonl purged at load alongside legacy events.jsonl); readChains/appendChain seam; merge dedupes by (sorted premises, conclusion), re-assertions append under the same arg_ id - core: deriveView mints implication nodes (name ⟹, statement via formatChainLine) plus premise→imp→conclusion arrows; clusters stay proposition-only (birthSessionPartition); chainsForSelection now groups STORED chains (chain rides iff every member selected) — independent arguments for one conclusion never union; chainsToGraph/chainsToEdges die - extraction: extractor submits chains natively (expandFindings deleted); auditor receives propositions only; supports fan-out gone - deletion: full death of a proposition kills every referencing chain; arg_-prefixed node deletes kill that chain; chainsRemoved stats - UI: every arrow renders the ⟹ double shaft; supports toggle + thickness slider and detail-card edge sections deleted (card keeps name + proposition); chain table + practice pipeline read stored chains - tests: 1188 green across the new seams |
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amosblomqvist
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8355fbabdb |
delete the mappings ledger — per-job in-memory resolution + notes fingerprint guard
The persisted (chatId, sourceId)→node table was a shared namespace across independent chunk/batch jobs: each chunk's extractor mints local ids fresh (p1..pN), so later chunks collided with earlier ones — propositions silently skipped as 'already resolved' (coverage checkpointed anyway: permanent silent loss) and edges resolved onto the wrong nodes (the 'everything links to everything' mush). Owner ruling 2026-09-29: mergeFindings resolves THIS job's ids in memory, nothing persists between jobs; cross-job identity is the auditor's linkTo verdicts alone. - contracts: NodeMapping dies; NotesSource.contentFp — sha256 of the text at the last run, the re-import guard (unchanged re-import = TRUE no-op, no model calls, no usage; changed text re-runs; legacy unstamped sources re-run once) - merger: job-local resolution map, in-submit duplicate ids skip once, edges resolve extractor-local ids only - ports/store: appendMapping/readMappings, LEDGER_FILES.mappings, rewriteLedgers.mappings gone (stale data/graph/mappings.jsonl just stops being read) - session-clusters: birthSessionOf is provenance-only — the legacy mapping-line fallback for provenance-empty notes nodes dies - deletion: no mapping rows to strip; stats lose mappingsRemoved - replay-layout batches nodes by first provenance point - graph.test pins the new independence semantics (re-merge re-creates; duplicate ids within one submit resolve once); extraction tests pin per-chunk merges + the fingerprint guard |
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amosblomqvist
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d1b46132b9 |
Wave 7 close-out: the embedding ledger seam dies; notes birth via mapping lines
Part 1 — the ledger + remnants interlude (master-dispatched, owner ruling 2026-09-23: nothing configures the graph beyond chat models): - The embedding ledger surface is gone: readEmbeddings/writeEmbeddings ports, the EmbeddingsLedger contract, EMBEDDINGS_FILE (config, store impls, graphRevision source list), and graph-deletion's vector-pruning step. On-disk data files stay untouched (inert history). - The extraction embedder seam dies wholesale: ExtractionPipelineDeps drops the embedder dep (chat-handler + backfill/import-notes stubs go with it), the 'embedding' phase leaves ExtractionPhase, the usage capture/persist helpers die, and stages.embedding leaves ExtractionRunUsage (historical records keep their shape — reads are lenient). Extraction is two stages again, like the local-embedder era. - Consumer-less remnants: latestQuizOutcomes + QUIZ_EVENT_KINDS, clusterContentId, matchClusterLabelings + Community + ClusterLabeling, the readClusterLabels/appendClusterLabel port seams + store impls + LEDGER_FILES.clusterLabels. NamingRunUsage/readNamingRuns STAY (standing ruling — the cost pill renders historical naming spend); clusterHue + MIN_CLUSTER_SIZE stay (live). - The 'labeler' role dies: BACKGROUND_MODEL_ROLES, ROLE_SLOT, ModelRole, the catalog pin projections, and the UI roster strings. RolePins keys shrink with the union. The notes birth fallback (owner-approved 2026-09-23, surfaced by the interlude's live smoke: production notes imports create provenance-EMPTY nodes (importNotes passes messages: null — the file's anchor is the mapping line), so the provenance-only birth rule left every imported file unclustered and invisible to the prober's session list, against the locked file-birth ruling. A provenance-empty node now births under its FIRST mapping line's chatId (ledger order); only notes-born nodes ever hit the fallback (chat nodes always carry provenance; a re-encountered node's link-append re-opens the provenance rule). Deletion-safe: mapping lines of deleted chats are stripped alongside their provenance. Live-verified on port 3004: a fresh notes import clusters under its src_ id with the file path as the label, end to end with no embedder. 845/845 tests, typecheck/lint/build green. EOF ) |
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amosblomqvist
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c86430e8bf |
Wave 7 chunk B: remove the embeddings machinery — the ladder collapses
The owner's wave-7 ruling: embeddings die entirely (git history is the
stash); clustering is birth-session derived (chunk A, 950ddfd), labels
are session names, and the prober's graph tools replace injection.
- settings: GraphSettings collapses to { enabled } — embedding,
embeddingModel, clustering, labeling all die. Migration story: stale
record keys are UNREAD and dropped by the sanitizer's reconstruction;
the next graph-section PUT (replace-whole) persists the collapsed
shape. The settings-panel GraphSection renders one master row.
- deleted: src/server/embeddings.ts (adapters, resolveEmbeddingPortFor,
embedNewNodes, embeddingPort, embeddingModelCatalog), the
GET /api/models/embeddings route, scripts/embed-graph.ts, tests for
all three, and the /api/models/embeddings picker surfaces in the UI.
- prices: EMBEDDING_PRICES overlay + callCost fallback die. cost-summary:
the embedding stage fold dies — back to three stages (extraction/
audit/naming) per the owner ruling; historical stages.embedding spend
in old run records is simply not displayed.
- ports: EmbeddingPort/EmbeddingResult/EmbeddingTask die. The embeddings
LEDGER surface (readEmbeddings/writeEmbeddings + EmbeddingsLedger +
EMBEDDINGS_FILE + graph-deletion's vector pruning) STAYS — inert data,
kept only so graph-context.ts compiles until Teacher's pass removes
it; the seam dies in the follow-up interlude.
- chat-handler (approved cross-lane unwiring, wave-6 precedent): the
extraction pipeline's embedder becomes a documented no-op (nothing
embedded, nothing spent, ledger untouched) until Teacher's pass
removes the phase; the graph-context injection dispatch gate, the
graphContext deps wiring, the setContextRespawn seam, and
turn-service's triggerGraphContext are gone — injection is dead
code pending Teacher's file deletions.
- scripts: backfill-graph/import-notes pass the same no-op embedder;
replay-layout derives clusters from birthSessionPartition (the same
partition the real settle uses) instead of the embeddings ledger.
- settings-body: parseGraphSettingsBody reads the master switch only —
old-shape keys in a body are ignored, not rejected; bad shapes 400.
- next.config: the @huggingface tracing-exclusion guards die with the
last reference.
Cross-lane flags: extraction.ts/graph-context.ts keep stale embed
comments + the embed phase until Teacher's full pass (their parallel
interlude owns those files — zero overlap kept by design);
semantic-clusters.ts + its test stay one more round (extraction.test.ts,
Teacher's file, still imports it — they delete it with the namer cases);
ChatSettings.graphContextTokens + the graph-context-control UI stay
until Teacher+UI.
Gates: tsc clean, eslint clean, 885/885 tests, build compiles.
Live-verified on the port-3004 dev tree: PUT /api/settings/graph with
dead keys collapses on write, bad shapes 400, GET reads {enabled: true},
/api/models/embeddings 404s.
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amosblomqvist
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f5edc7f0a5 |
Semantic topic clusters: local embeddings replace Louvain
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). |
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amosblomqvist
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3a1c18b9de |
Inference-depth anchoring playground: vertical + radial modes
The graph's follows/supports edges encode derivation (premise -> conclusion); the layout can now express that rank spatially, as a session-only playground toggle (nothing promoted yet): - inferenceDepths: longest chain from a base node, CYCLE-SAFE by SCC condensation (Tarjan, iterative) — the DAG property is typical, not guaranteed; cycle members share their component's depth (mutual support = equal footing). O(V+E), pure, deterministic. - DepthAnchor force: per-node target scalar — vertical mode rows (baseline at the anchor centroid, arrows up), radial mode rings (foundations center, outer boundary = edge of knowledge). The rank is computed, not simulated: pairwise up-forces can't give baselines. - Mode projections: gravity x-only in vertical / dropped in radial; cluster pull x-only in vertical / tangential-only in radial; the anchor re-blend preserves user arrangement in the FREE dimension only (x / angle) — meaning owns the constrained axis, memory owns the free one. - setPhysicsTuning reheats (alpha 1): toggling a mode re-forms the graph live and commits the new rest state; drag release is springy along the constrained axis (node returns toward its level/ring). - Sweep on the real graph: strength 0.8 = 215/216 arrows correct with organic sag; 1.5 = crisp rows. 174 base nodes, max chain depth 7, zero cycles in current data. replay-layout --depth=<mode> bakes a mode into the ledger for rest-state experiments. |
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amosblomqvist
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975a78a304 |
Cluster gravity: per-cluster centroid pull force in the engine
The 'virtual node' realized as a centroid force: two allocation-free O(n) passes per tick (membership resolved once at sim creation; Float64Array sums). Measured indistinguishable from force-off at 338 nodes (271ms vs 272ms per 400-tick settle). - createGraphSimulation: SimOptions.clusterPull + linkStrength + velocityDecay (physics controls plumbing); degree-scaled link stiffness so linkStrength=1 is exactly d3's default - settleGraphLayout split into layout-settle.ts (it computes the Louvain partition for the pull); layout.ts stays browser-barrel-pure - barrel no longer re-exports clusters.ts: graphology + louvain are fully out of the client bundle (verified against built chunks) - replay passes the per-batch partition; CLUSTER_PULL_STRENGTH=0.15 tuned by sweep: cluster spread 63->36 world units, centroid separation and total span unchanged (no blob merge, no collapse) |
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amosblomqvist
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7eceb58303 |
Engine unification: d3-force replaces forceAtlas2 everywhere
One engine owns the equilibrium: the merge settle and (next commit) the live drag both run createGraphSimulation — d3-force link springs, 1/d charge, weak centroid gravity — so a drag's rest state IS the server's rest state. The FA2-era anchor mechanism survives as a post-tick POSITION-SPACE re-blend (retention 0.85): d3's forceLink is a Hooke spring (strength*(d-L)*alpha), which overpowers any force-space anchor at long range — the re-blend is alpha-independent and always wins as the sim anneals (the 675-unit drift bug). Gravity retuned for d3's 1/d many-body falloff (bootstrap 0.2 / incremental 0.12: cluster spacing lands ~400 world units, the FA2-era density). Rim orphans seed (and anchor) at 1.7x the CONNECTED core's mean radius — a max-span-based rim fed back on itself and ran the layout away to 6000 units. Replay: 338 positions in 1.6s, old-node shift within a batch 4.8 (FA2: 23). |
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amosblomqvist
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0c14ea425d |
Option A: incremental anchored force layout, persisted server-side
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
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