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