User-facing live-sim controls (settings panel, Physics section):
node repulsion, edge attraction, edge length, central pull, cluster
pull, friction — session-only number inputs feeding createGraphSimulation
(the SAME engine the server settle runs, so the feel IS the physics).
Changing a value rebuilds the sim from current positions; drag pins
(fx/fy live on the node objects) survive; a mid-settle change re-anneals.
The graph-view FA2 bootstrap fallback is rewritten on incrementalLayout
(d3-force): the last graphology import in the shell is gone.
User feedback round 1 on the splat regions:
- Double counting: per-node gradient discs stacked with the edge-stroke
dilation wherever nodes sat on edges (hub hot spots). A cluster is its
CONNECTED skeleton — the region is now the dilated intra-cluster edge
network ONLY (round caps make line-end points discs), per the user's
definition. No per-node discs at all.
- The 'blur' was no blur: bilinear upscale of a 256px bitmap produced
tent-ramp chunkiness at zoom (the low-quality-JPEG look). Now a REAL
blur: 3 box-blur rounds on the premultiplied bitmap (separable running
sum, pure + unit-tested; premultiply keeps halos out of transparent
space). The upscale now has nothing left to make chunky.
- Live dev controls: number inputs (not sliders) in the settings panel —
dilation (screen px at fit), blur (bitmap px), bitmap resolution,
edge alpha. Session-only React state, never persisted; the renderer's
sanitizeRegionTuning makes bad/empty values safe. Verified end-to-end
through the real input (dilation 28 → 60 took effect).
- Premultiply un-recovery bug caught live: c = pm/a*255, not pm/a (the
first version rounded every color to black; regions rendered as
dark blobs with alpha 185).
- Region canvas: willReadFrequently (Chrome keeps it on the CPU for the
per-rebuild getImageData); defaults dilation 55 → 28 after measuring
screen coverage (63% → 55%).
- Perf: 120fps sustained through a drag with blur + rebuild-every-3rd-
frame (45 frames / 360ms measured), zero idle frames after settle.
The renderer grows a live d3 sim (createGraphSimulation, shared with
the server settle): pointerdown on a node pins fx/fy and pointer capture
(preventDefault kills the compat mousedown, so d3-zoom never pans); the
first CLICK_SLOP-exceeding move reheats to alphaTarget 0.3; release
un-pins and the sim anneals (release-and-relax) — alpha < 0.005 settles
it, a 250ms debounced onCommit PUTs the rest state. Verified live: 123fps
during a 320ms drag (regions rebuilding every 3rd frame), 85-tick settle,
then zero idle frames. A slop-free press stays a click (select, no reheat,
no commit). PUT /api/graph/positions sanitizes (finite coords, known ids)
and if the graph grew mid-drag runs ONE incremental settle with the
client's arrangement as anchors (50-id PUT test: anchored drift 0.15).
Cluster regions swap convex hulls for a low-res world-space SPLAT bitmap:
per-member radial-gradient discs (alpha 0.2) + intra-cluster edges as
round-cap strokes (Minkowski dilation — concave shapes finally render),
upscaled with bilinear smoothing (the upscale IS the blur, no ctx.filter:
Safari). One tiny blit per frame replaces 32 clusters x 4 offset
Path2D polygons re-rasterized at DPR 2 (the old GPU coil-whine path);
during the live sim the bitmap rebuilds every 3rd frame. cluster-geometry.ts
retires convexHull/offsetPolygon/traceRoundedPath (tests follow; clusterHue
stays). Region labels stay (centroid + clusterHue, inverse-gated on zoom).
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.
- LABEL_GAP 6 -> 2 (user: labels sit way too far below their nodes).
- Hover glow is now PROPORTIONAL to the disc — outer radius = node radius
x 1.7 (GLOW_SCALE), matching the blur-a-copy-of-the-disc mental model,
instead of the old constant +6px pad that read huge on small nodes and
thin on big ones. GLOW_ALPHA 0.45 -> 0.3.
- Hover-OUT fade was broken by construction: draw() gated the glow on
hoverId, which nulls instantly on leave, so the 180ms fade-out ran
invisibly and the glow popped off in one frame. New hoverNode field
outlives hoverId through the outgoing fade (cleared when the fade
completes); verified live: 8 distinct frames over ~200ms then stable.
- Sliders rescaled per spec: ALL five are now log-scaled 0-100 with the
default dead-center at 50 (ranges chosen as default/4..default*4:
node/arrow/label size 0.5-8, edge width 0.25-4, labelZoom 0.0625-4),
coarse step 5 (21 stops; labels-until-zoom was "way too granular" at
201). Generic toSliderPosition/fromSliderPosition replace the
labelZoom-only pair; sanitize clamps follow the same range constants;
size sliders display compact values ("2", "1.6", "0.75").
EOF
- Defaults per user: nodeSize 2, edgeWidth 1, arrowLength 2, labelSize 2
(labelZoom 0.5 stays — reads as the "1x" they confirmed good).
- Label size slider floor 3 -> 1 so the default 2 is not the smallest
value; sanitize clamp widened to match.
- Cluster hull glow (layered low-alpha fills) removed for now: it read as
jagged up close (straight-line hull approximation at high zoom) and
does not belong until the layout settles. The solid viewer-relative
border and the inverse-gated region labels stay. HULL_FILL_LAYERS
constant deleted; hullShapes cache carries only the stroke path now.
- Saved render-settings.json reset so the new defaults apply on next load.
EOF
The defaults were calibrated in the screen-fixed era; world-scaling renders
sizes at setting x k/kFit, so at the default label gate (2x fit) everything
read ~2x too big ("labels way too large even at the minimum"). Fit-zoom
normalizes layout scale away, so the fix belongs in sizes, not layout:
spreading nodes further apart in world units changes nothing at fit.
- Defaults: nodeSize 6 -> 4, arrowLength 5 -> 4, labelSize 12 -> 7.
- Clamps/slider ranges widened at the low end: nodeSize 1-14 (step 0.5),
edgeWidth 0.25-4 (step 0.25), arrowLength 1-15 (step 0.5),
labelSize 3-24 (step 0.5).
- GLOW_PAD 9 -> 6 (halo dominated small discs), REGION_LABEL_SIZE 18 -> 14.
- Tests updated for the new clamp bounds plus a low-end pass-through case
(403/403). The saved render-settings.json still shadows defaults by
design; the local copy was reset so the new defaults showed immediately.
Fixes the zoom frame-rate collapse and rebuilds draw() around a single
camera transform, per the user's Obsidian-style sizing proposal.
Bug fix first: the eased zoom leaked a queued rAF callback per frame --
advanceZoom applies each step through d3-zoom, whose zoom event called
markDirty() from inside the tick loop, scheduling an extra draw while the
loop scheduled its own. Draws multiplied per displayed frame; sustained
wheel ran at ~20fps against a 120Hz display. markDirty now skips
scheduling while inTick (verified: 62 frames/500ms during a 28x zoom
burst, matching pan).
World-space model: every draw call now runs in graph coordinates under
one setTransform(k). Sizes are defined as screen-px-at-fit and converted
once per geometry build (/ kFit), so nodes, node labels, arrowheads and
the hover halo scale with the graph as you zoom (0.25x painted area at
half zoom, exactly k^2) while edge widths and hull borders stay
viewer-relative hairlines (/ k). Cluster hull geometry (convex hull +
three offset fills + solid boundary -- dashes dropped for now) is built
as cached Path2Ds per data/visibility/settings change; camera moves do
zero geometry math, making zoom per-frame cost identical to pan. Label
wrapping runs once per build, not per frame. Region labels stay
viewer-relative (18px at any zoom) as UI chrome. Picking radius scales
with the world-sized discs.
Glide feel: ZOOM_EASE_MS 120 -> 45, convergence 0.1% -> 0.2%; a notch now
settles in ~260ms instead of ~750ms. Resize still paints synchronously.
Also fixes barrel-law lint violations from the settings wave (import
from @/src/core and @/src/server, not deep module paths).
Five refinements to the hand-rolled renderer, all user-directed:
1. Settings are SERVER-persisted (data/render-settings.json via new
GET/PUT /api/graph/render-settings) - one source of truth for every
browser, replacing localStorage. The client loads once after mount,
saves debounced on user changes, and never lets a slow GET clobber a
faster user (or mounting PUT defaults over the server copy). The
shape/defaults/sanitizer moved to src/core/render-settings.ts - pure,
shared by client, server store, and tests; every disk/network value
passes through sanitizeRenderSettings.
2. New "Label size" control (default 12px - the previous hardcoded size).
Font, wrap width, and line height all scale; verified live: +76k px
with the label gate open.
3. "Labels until zoom" slider reworked: log-scaled over 0.0625-4 so the
useful band (0.25-0.5 camera-ratio units) sits at 33%/50% of the
track instead of crammed at the far left of the old linear 0.25-4
slider. Display units are normalized: the default 0.5 reads as "1x",
0.25 as "0.5x". The underlying labelZoom semantics are unchanged,
so existing values survive.
4. Smooth wheel zoom: d3-zoom instant per-notch jumps (x1.2, bang) are
replaced by an eased glide - wheel events accumulate a cursor-anchored
target scale and each tick eases the camera toward it (exponential,
120ms constant, frame-rate independent). Pan/pinch stay d3-owned; a
pan cancels a glide in progress. Verified live: 8-frame glide.
5. Resize blanking fixed (graph vanished for the duration of a window
drag, reappearing ~300ms after). Cause: every resize event
reallocated the canvas backing store - which CLEARS it - and the
redraw was deferred to rAF, which live resizes starve via relayout,
so the canvas sat wiped for the whole drag. Fix: the ResizeObserver
callback now redraws SYNCHRONOUSLY after reallocating (verified via
a probe RO firing in the same delivery batch: canvas fully painted).
kFit (the label gate 1x reference) is also recomputed on resize from
the now-cached world bbox - the camera itself still persists.
tests/render-settings.test.ts: 10 tests pinning the sanitizer (garbage/
partial/clamps, legacy no-labelSize records) and the slider mapping
(default dead-center at 500, monotonic, exact round-trips, display
units). 402/402 green; typecheck, lint, build pass.
Implements Option B from docs/research/graph-rendering.md. sigma.js v3
(WebGL) is replaced by one canvas, one rAF loop with a dirty flag, and
d3-zoom for the camera — eliminating the entire bug class from the
sigma-era bolt-on architecture:
- Hull/node desync during pan (two independent render loops) is now
structurally impossible: hull fills, dashed hull strokes, edges with
arrowheads, node discs, region labels, node labels, and hover glow
are all drawn in ONE frame under ONE camera.
- The settings-change canvas-sizing race (everything shifting up-left)
is gone: settings changes only redraw; the canvas and camera persist
(verified live: camera identical to 15 decimals across a slider drag).
- The GPU floor is gone: idle schedules NO frames at all (verified via
pixel-identity over 600ms idle); pan redraws exactly once per frame.
components/graph-canvas.ts: GraphCanvasRenderer class plus pure helpers
(zoomRatioOf, labelAlpha, fitTransform, arrowGeometry, pickNearest).
The sigma camera-ratio convention (1 = fit, smaller = zoomed in) is kept
verbatim so persisted labelZoom settings survive the swap; node labels
and cluster region labels cross-fade over the same LABELS_FADE_SPAN
(0.5, unchanged). Picking is a nearest-node distance check with the
10px pad that replaces the old padded-picking vertex shader. Hull math
stays in components/cluster-geometry.ts, reused as-is. No ctx.filter,
ever.
graph-view.tsx keeps every feature: fetch/refetch on runs-empty, FA2
run-then-freeze layout, localStorage render settings + sanitizers,
search filtering with edge drops and card-close, detail card with
flipped anchoring and per-source provenance, settings panel, import
button, pipeline status chips. Only the renderer plumbing changed.
tests/graph-canvas.test.ts pins the pure math: ratio direction, label
gate + inverse complement (alphas sum to 1), fit transform padding,
arrowhead tip-on-disc-edge and symmetry, picking pad/ties/null cases.
Live-verified end-to-end on the real 338-node graph (dev server
port 3002): single canvas, paint at fit, hover cursor+glow+fade, click
card open/anchored/close, stage click, search filter to zero with hint,
label gate opens via slider and zoom, cluster-labels toggle, zoom-to-
cursor 0.56px anchor drift, camera persistence across settings, zero
idle repaints. sigma dependency removed from package.json; d3-zoom and
d3-selection added.
Note: the settings feed effect needed isEmpty in its deps — without it
the renderer mounted with settings=null and every draw early-returned
(blank canvas); caught live, not by typecheck.
Three problems from the first cut (user report 2026-09-13), all rooted
and fixed:
1. Boundaries reshaping on zoom — an inward offset normal. In y-down
screen coordinates, monotone chain yields clockwise-on-screen hulls,
whose OUTWARD normal is (dy, -dx); the code used (-dy, dx), so the
14px padding pulled every hull vertex 14-20px INWARD. Zoomed in this
mostly passed; zoomed out, once a cluster projected smaller than ~2x
the pad, vertices crossed the centroid and the polygon self-
intersected — spiky garbage re-forming every frame. Geometry moved to
components/cluster-geometry.ts (exported, unit-tested) with the
corrected normal; tests pin the direction (offset moves every vertex
AWAY from the centroid; stays sane when the hull is smaller than the
pad; hull orientation asserted clockwise-on-screen).
2. GPU ~100% + audible coil whine on any interaction — the hull redraw
was hooked to sigma's afterRender, which fires for EVERY render
including ~a dozen hover-animation frames per hover, and each redraw
rasterized ~32 fills through ctx.filter blur(12px), a GPU-heavy
full-canvas filter. Now: redraws happen ONLY on camera updates and
resizes (hover leaves the hull canvas untouched — verified live),
and the blur is replaced with layered low-alpha fills (soft edge at
a fraction of the cost, no canvas filter at all).
3. Cluster labels cluttering the view — a persisted 'Cluster labels'
checkbox in the rendering settings (hulls stay, text toggles).
377/377 tests, typecheck, lint, build green. Live-verified: hover does
not repaint hulls, zoom does; far zoom-out yields 3 contiguous tinted
regions (no fragmentation); toggle clears/returns labels and persists.
Two custom canvas layers around sigma's own stack (DOM order: hulls
behind everything; region labels above nodes, below node labels).
Per cluster (vision section 1): convex hull (monotone chain) of member
viewport positions, offset outward 14px, rounded corners, a blurred
low-opacity fill (ctx.filter, graceful degrade to flat fill) plus a
dashed boundary stroke, and the LLM label at the centroid. Stable hue
per cluster id (content hash) — a region keeps its color across
reshuffles because the id only changes when the members do.
Geometry is a pure function of positions at draw time: every
afterRender re-derives hulls through the current camera, so pan/zoom/
relayout can never invalidate it (the boundary decision pays off: no
stored geometry, nothing to recompute after a future physics change).
The inverse gate: the cluster label layer's opacity is the exact
complement of the node-label layer's over the fade span of THE zoom
control (labelZoom, default 0.5x) — the two label systems never
coexist.
Live-verified in the browser: hulls painting behind edges; region
labels above nodes; zoom-in crossfades cluster 1 -> 0 as node labels
0 -> 1 (0.176 + 0.824 mid-fade); zoom-out restores; hull pixel count
changes with zoom (geometry follows the camera); zero console errors;
layers removed on renderer teardown. 372/372 tests, typecheck, lint,
build green.
Also named the real graph: one 11.5s labeler call minted all 32
region labels for the 338-node notes graph (Relational Databases & SQL,
Differential Forms, Sales as Uncertainty Reduction, ...).
The most suitable default is the stricter end — labels only once
zoomed in past 2x fit (user-decided 2026-09-13). The slider window
extends below it (0.25x) so the default is no longer the floor.
The label-visibility zoom threshold (was the LABELS_CAMERA_RATIO=1
constant) becomes the fourth persisted setting: labels appear when the
camera ratio is at/below it (1x = fit zoom; slider 0.5x-4x, shown with
an x suffix). Deliberately THE single zoom knob per the cluster design
(vision section 1): cluster labels will fade in over the same span as
node labels fade out, gated inversely on this same setting.
Live-verified: at a zoomed-out camera (labels previously hidden),
raising the threshold to 4x rebuilds and re-shows labels without any
camera movement; resetting restores the fade. 355/355 tests,
typecheck, lint clean.
Three sliders behind a gear in the search panel (user-decided
2026-09-13), persisted per browser in localStorage with clamped
sanitizing on load. Default node size dropped 8 → 6 for dense graphs.
Mechanics: the mount effect is split — the data effect builds the
graphology graph + one frozen forceAtlas2 pass per snapshot; the render
effect mounts sigma and re-runs on settings change only. Sizes are
stamped onto the same graph instance (layout never recomputed), and the
arrowhead program is constructed per rebuild with ratios solved from
the settings (head px = thickness × lengthToThicknessRatio × 2; wideness
keeps the stock 0.8 shape). The camera position carries across rebuilds
via a ref, so a slider tweak never re-fits or re-lays-out the view;
useDeferredValue smooths slider drags.
Live-verified in the browser: sliders persist to localStorage, the
renderer rebuilds with zero console errors, hover/picking survives the
rebuild, and a zoomed-out camera stays zoomed out across a settings
change (labels-gate opacity as the observable). 355/355 tests,
typecheck, lint, build green.
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.
Some labels (clustered nodes: Flux, The signifier rules the subject,
The body as window onto the thing-in-itself) appeared later in zoom than
others, without fade. Root cause: sigma's label grid — viewport cells
of labelGridCellSize (100px default) compete, only ceil(labelDensity /
ratio^2) winners per cell draw (one at fit with default density 1) —
so clustered nodes' labels were culled until zoom changed the quota,
then popped in with the global fade already complete.
labelDensity: MAX_SAFE_INTEGER turns the quota off. The camera-ratio
gate (LABELS_CAMERA_RATIO + LABELS_FADE_SPAN) is now the ONLY label
culling: every label appears at the same zoom with the same fade —
the wave-1 'all labels at once' intent, finally true.
Verified pixel-level at fit view: all 31 node labels render, including
the three previously-missing ones; no console errors.
The background extraction pipeline is invisible on the home surface —
essential observability per the user's directive: the graph view must
show what is currently running (extracting / auditing / merging) and
for which chat.
- extraction.ts: module-level registry of in-flight runs (chatId,
phase, startedAt), updated at each phase transition in runExtraction
and cleared in finally (done or failed). extractionStatuses() is the
read; one process, one registry.
- GET /api/graph/status: thin transport over the registry, chat titles
joined from the chat store.
- graph-view: polls every 2s and shows one chip per running pipeline
(spinner + phase + title + elapsed seconds, bottom-left); when a run
finishes (some -> none) the graph refetches, so merges land live.
Status is cosmetic — poll errors never surface.
- Unit test drives a mocked pipeline run and observes the registry
mid-flight: 'extracting' during the extractor's generate, 'auditing'
during the auditor's, empty after.
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.
The top-right overlay doubles as the state legend and the filter
surface: a search box (matches name or statement, case-insensitive)
plus one row per node state in reading order (taught, known, missed,
don't know, candidate) with its color dot, label, and total count.
Clicking a row toggles that state's visibility.
Filtering flows through sigma's official nodeReducer/edgeReducer
settings: hidden nodes drop out of rendering, hover, picking, AND
labels; edges drop when either endpoint is hidden; an open detail card
closes if its node is filtered out. Pure predicate (isNodeVisible) is
exported and covered by 7 tests; the reducers just consume its
verdict. Verified live: search 'Nietzsche' 5457->1687->5457 label px
(exact restore), known toggle drops 13 discs+labels and restores,
nonsense query shows the 'No matching nodes.' hint with zero labels,
counts 0/13/0/0/10 match the ledger.
Fixes the hover flicker the maintainers' way (jacomyal/sigma.js#1493):
sigma v3 picks nodes by reading a single pixel from a picking
framebuffer rendered at HALF the CSS resolution, and has no setting
for hit padding. Small nodes get tiny, ragged hit edges, and our glow
halo (9px beyond the disc) was NOT pickable — moving the cursor from
the disc onto its own halo de-hovered it, an oscillation loop.
NodeCircleProgram subclass (registered via nodeProgramClasses)
replaces only VERTEX_SHADER_SOURCE: a verbatim copy of sigma 3.0.3's
circle vertex shader that adds PICKING_PAD_PX (10) of radius under
#ifdef PICKING_MODE alone. The visible pass never takes that branch,
so rendering is pixel-identical (verified headless); the pickable
disc is disc + 10px, covering the whole hover halo, so the halo is
now hoverable and small candidate nodes are comfortable to hit.
sigma/rendering is imported dynamically (its ESM build touches
WebGL globals at module scope; SSR-safe like the sigma import).
This replaces the reverted prototype-patch approach (f12480e).
sigma v4 ships this officially as the nodePickingPadding setting —
noted for a future upgrade.
Root cause: sigma's getNodeAtPosition reads the picking framebuffer,
which is rendered at HALF the device resolution
(pickingDownSizingRatio = 2 * pixelRatio). Small nodes' hit circles
are a couple of device pixels across in that buffer with ragged,
quantized edges — near a node boundary, tiny cursor movements flip
the hover state on/off, and each flip makes sigma clear the hover
layer immediately. That state churn is the flicker; it survived every
animation change because it was never in the animation.
Mitigations:
- patchNodePicking() replaces Sigma.prototype.getNodeAtPosition with
a smooth distance test (rendered radius + HIT_PAD_PX = 6px) built on
public renderer APIs only (getGraph, getNodeDisplayData,
framedGraphToViewport, scaleSize). No ragged edges, and small
candidate nodes get roughly double the hoverable area.
- Leave-debounce (90ms): when hover drops, hold repainting the
captured hover paint at the current fade (sigma would otherwise
clear the layer the instant hoveredNode flips to null), and only
fade out if the cursor hasn't bounced back within the window. A
re-enter cancels the fade, so boundary oscillation never visibly
dims anything.
The instant muted->bright color swap felt abrupt next to the fading
halo. The hover name is again drawn at partial alpha over the muted
resting label, using the SAME transition factor as the halo — text
and glow fade in/out in sync. Because every enter/leave interpolates
from the current fade value, rapid hover toggles at a node's hit
boundary glide instead of snapping (the flicker-damping fix).
- The halo no longer grows during the fade: radius is constant at
size + 9px; only its opacity fades in/out over ~180ms.
- The hover name is drawn opaque in the bright color instead of
cross-fading over the muted resting label. Partial-alpha text
oscillated whenever hover toggles rapidly at a small node's hit
boundary (sigma fires enterNode/leaveNode on every state change) —
an un-animated color can't flicker.
- The glow no longer pulses: it's a static halo (9px beyond the disc,
0.45 alpha at the edge fading outward) in the node's state color.
- Hover enter/leave now cross-fades over ~180ms instead of appearing
instantly: entering schedules sigma renders so drawHover repaints at
the interpolated fade; leaving draws through a repainter captured on
the last hover paint (sigma stops calling drawHover once unhovered).
The text cross-fades too — the brighter hover name is drawn at
partial alpha over the muted resting label on the layer beneath.
- The halo starts flush at the node disc edge (was size+1, leaving a
dark gap ring that read as a gray border between node and glow).
- Both fade directions cancel each other and stop on completion, so
there is no continuous loop — idle CPU stays near zero.
- defaultDrawNodeHover no longer paints a background box: the hovered
node now pulses a soft radial-gradient halo ring in its own state
color (evenodd punch-out keeps the node disc untouched), phase driven
by performance.now() inside the drawer.
- The hovered label text brightens (muted-foreground -> foreground) at
identical geometry — drawName is shared by both drawers so nothing
shifts when hover begins/ends.
- The pulse is animated by a rAF loop that only runs while a node is
hovered (enterNode starts, leaveNode/leaveStage stop, cleanup
cancels) — idle CPU stays near zero, preserving run-then-freeze.
- roundedRect removed with the pill (its only remaining consumer).
- roundedRect typo: the first arcTo's second control point used y+width
as the x-coordinate (y + width instead of x + width). Since arcTo
tangent math is in absolute coordinates, the pill outline sprouted a
stray wedge/notch whose size scaled with the pill's on-screen
position (diagnosed live by the tester subagent: ~1000px left spike
on a top-right node, right-side bites near the left edge).
- Labels now fade instead of popping: fully visible at fit zoom or
closer, then the labels canvas layer's opacity is interpolated across
a 0.5 camera-ratio zoom span before renderLabels switches off, with
the setSetting call guarded so pans don't spam refreshes.
labelRenderedSizeThreshold gated each node's label by its own rendered
size, so big (taught) nodes showed names several zoom stops before
small (candidate) ones. Zero the per-node threshold and instead toggle
renderLabels from the camera ratio: every name appears at fit zoom or
closer and they all vanish together when zooming further out. Hover
still reveals any node's name regardless of zoom.
- Custom sigma label drawers replace the defaults: every label renders
the node name word-wrapped under the node (max 170px line, overlong
words hard-broken, never truncated) instead of one long strip to the
right of the node.
- Hover swaps sigma's hardcoded white box for a dark rounded pill using
the app's popover tokens; hover always shows the name, even below the
zoom threshold.
- labelRenderedSizeThreshold 12 -> 6 (names are short now) and labels
use the app's body font at weight 500.
- Click card anchors just below the clicked node's viewport position
(flipping above near the bottom edge, clamped horizontally, measured
in a layout effect so the flip never flashes); any pan/zoom dismisses
it via the camera 'updated' event.
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 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