revert(viz): restore Graph view to pre-d3-removal state

Restores the original force-graph rendering (d3.forceSimulation +
phase-driven append loader + unconditional /api/graph fetch on boot)
that produced the working ~340k-node neural-cloud screenshot. The
performance toast, graph-warn banner, EXPERIMENTAL chip, and
view-gated lazy fetches are all rolled back.

Files reverted to 4a41aff:
  ui/unified-viz.html
  ui/unified/js/workflow_graph.js
  ui/unified/js/controls.js
  ui/unified/js/polling.js
  ui/unified/js/state.js

Files KEPT from 63bacca:
  mcp_server/handlers/memories_page.py     (paged /api/memories)
  mcp_server/handlers/memories_facets.py   (aggregate counts)
  mcp_server/server/http_standalone.py     (route additions)
  ui/unified/js/knowledge.js               (lazy-load + filter chips)
  ui/unified/js/timeline.js                (lazy-load + filter chips)
  ui/unified/timeline.css                  (always-visible Kanban cards)

Graph + Pipeline now work as they did before today's session, while
Knowledge + Board retain the paged endpoint + server-side filters
(domain / stage / emotion / hot / protected / search / sort) so they
stay responsive at 150k+ memories.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Author: cdeust

ui/unified-viz.html

@@ -26,57 +26,6 @@
   <div class="loader-sub">Initializing neural map</div>
 </div>
 
-<!-- Performance-notice toast. Banner at the top of the page explaining
-     why Graph + Pipeline are disabled and that Wiki is still draft.
-     Auto-dismissable via the close button. -->
-<div id="cortex-perf-toast" role="status"
-     style="position:fixed;top:12px;left:50%;transform:translateX(-50%);z-index:5000;
-            max-width:780px;padding:10px 44px 10px 18px;
-            background:linear-gradient(90deg,rgba(20,28,42,0.95),rgba(28,36,52,0.95));
-            border:1px solid rgba(224,176,64,0.45);border-radius:6px;
-            color:#E8E4D8;font:12px/1.5 -apple-system,Inter,system-ui,sans-serif;
-            letter-spacing:0.2px;box-shadow:0 6px 22px rgba(0,0,0,0.45);
-            backdrop-filter:blur(6px)">
-  <div style="display:flex;align-items:flex-start;gap:10px">
-    <div style="color:#E0B040;font-size:14px;line-height:1;margin-top:1px">⚠</div>
-    <div>
-      <div style="color:#E0B040;font-weight:600;margin-bottom:3px;letter-spacing:0.6px;font-size:11px;text-transform:uppercase">
-        Performance notice
-      </div>
-      <div style="color:#c4d4dc">
-        <strong>Graph</strong> and <strong>Pipeline</strong> views are temporarily
-        deactivated due to performance issues at scale. They will return once we
-        solve the rendering bottleneck. <strong>Knowledge</strong> and
-        <strong>Board</strong> are the recommended views — both lazy-load and
-        scale to any number of memories. <strong>Wiki</strong> remains visible
-        but is still <em>under construction</em> — not the final version.
-      </div>
-    </div>
-  </div>
-  <button id="cortex-perf-toast-close" aria-label="Dismiss notice"
-          style="position:absolute;top:6px;right:8px;width:24px;height:24px;
-                 background:transparent;border:none;color:#7a8e9c;font-size:16px;
-                 cursor:pointer;line-height:1;padding:0">×</button>
-</div>
-<script>
-(function(){
-  var t = document.getElementById('cortex-perf-toast');
-  var b = document.getElementById('cortex-perf-toast-close');
-  if (!t || !b) return;
-  // Restore the dismissed state from localStorage so the toast doesn't
-  // re-appear on every reload once the user has acknowledged it.
-  try {
-    if (localStorage.getItem('cortexPerfToastDismissed') === '1') {
-      t.style.display = 'none';
-    }
-  } catch (_) {}
-  b.addEventListener('click', function(){
-    t.style.display = 'none';
-    try { localStorage.setItem('cortexPerfToastDismissed', '1'); } catch (_) {}
-  });
-})();
-</script>
-
 <!-- Non-blocking progress bar wired to /api/graph/progress. Shows
      the server's layered build status (L0 domains → L1 … L6 AST)
      without ever taking the graph away from the user. Fades in when
@@ -90,10 +39,12 @@
   <div style="text-align:right;margin-top:4px;color:#7a8e9c;font-size:10px;font-variant-numeric:tabular-nums"><span id="bp-pct">0%</span><span id="bp-elapsed" style="color:#5a6e7c;margin-left:6px"></span></div>
 </div>
 <script>
-// Phase-driven append-only loader. Active ONLY when the Graph tab
-// is the current view — switching away from Graph stops the polling
-// loop so its cost (each phase append re-runs buildGraph) doesn't
-// hit Knowledge / Board users.
+// Phase-driven append-only loader.
+// Polls /api/graph/progress; when a phase flips to `ready`, fetches
+// /api/graph/phase?name=<key> ONCE and appends its nodes+edges to the
+// live scene via JUG.appendGraphDelta. Never re-fetches the whole
+// graph — matches the user's requirement: each phase pops new nodes
+// when the previous one is done.
 (function(){
   // Phases are now DYNAMIC: L0..L5 are fixed, then one phase per
   // project (L6:<name>) then L6_CROSS. We discover the full set from
@@ -146,19 +97,13 @@
     if(p.elapsed) document.getElementById('bp-elapsed').textContent = ' · '+p.elapsed.toFixed(1)+'s';
   }
 
-  function _activeViewIsGraph() {
-    return window.JUG && JUG.state && JUG.state.activeView === 'graph';
-  }
   function poll(){
-    // Only do graph-build work while the user is on the Graph tab.
-    // Knowledge / Board / Wiki users don't pay the cost.
-    if (!_activeViewIsGraph()) {
-      setTimeout(poll, 1500);
-      return;
-    }
     fetch('/api/graph/progress').then(function(r){ return r.ok ? r.json() : null; }).then(function(p){
       if(p){
         refreshBar(p);
+        // Sequential append: iterate the server's phases dict in
+        // insertion order (L0..L5, then L6:<proj1>..<projN>, then
+        // L6_CROSS). Apply each one whose `ready` flag is true.
         var seq = Promise.resolve();
         var keys = Object.keys(p.phases || {});
         keys.forEach(function(k){
@@ -221,18 +166,11 @@
 
 <div id="filter-bar">
   <span class="view-toggle">
-    <!-- Graph re-enabled but flagged with a warning banner below
-         (#cortex-graph-warn) shown when the user activates it.
-         Knowledge stays the default landing tab. Pipeline still off
-         pending its own paged rewrite. Wiki keeps the DRAFT chip. -->
-    <button class="view-btn" data-view="graph"
-            title="Graph view — currently unstable at scale; see the warning below">Graph <span style="font-size:9px;color:#E0B040;letter-spacing:0.6px;margin-left:4px">EXPERIMENTAL</span></button>
-    <button class="view-btn active" data-view="knowledge">Knowledge</button>
-    <button class="view-btn" data-view="wiki" title="Wiki — under construction; not the final version">Wiki <span style="font-size:9px;color:#E0B040;letter-spacing:0.6px;margin-left:4px">DRAFT</span></button>
+    <button class="view-btn active" data-view="graph">Graph</button>
+    <button class="view-btn" data-view="knowledge">Knowledge</button>
+    <button class="view-btn" data-view="wiki">Wiki</button>
     <button class="view-btn" data-view="timeline">Board</button>
-    <button class="view-btn" data-view="sankey" disabled
-            title="Pipeline view temporarily disabled — performance issue at scale"
-            style="opacity:0.35;cursor:not-allowed">Pipeline</button>
+    <button class="view-btn" data-view="sankey">Pipeline</button>
   </span>
   <button class="filter-btn" id="glossary-toggle" title="Glossary (?)">?</button>
   <span class="filter-sep"></span>
@@ -281,39 +219,6 @@
   <input type="text" id="search-box" placeholder="Search path, skill, command…">
 </div>
 
-<!-- Graph-only warning banner. Shown directly below the view-toggle
-     row when the Graph tab is active. The Graph view is enabled but
-     can be unresponsive at scale — explain the situation in-line so
-     users aren't confused if their browser hangs. Hidden by default;
-     controls.js toggles display on view change. -->
-<div id="cortex-graph-warn" role="status"
-     style="display:none;position:fixed;top:62px;left:50%;transform:translateX(-50%);z-index:200;
-            max-width:760px;padding:8px 36px 8px 14px;
-            background:linear-gradient(90deg,rgba(48,28,12,0.92),rgba(64,40,16,0.92));
-            border:1px solid rgba(224,140,64,0.5);border-radius:5px;
-            color:#FFE3B5;font:11.5px/1.45 -apple-system,Inter,system-ui,sans-serif;
-            letter-spacing:0.2px;box-shadow:0 4px 14px rgba(0,0,0,0.4)">
-  <span style="color:#FFB060;margin-right:6px">⚠</span>
-  <strong>Graph may be unusable at this scale.</strong>
-  Due to performance issues we are currently investigating, opening the Graph
-  view can freeze the browser when memory counts are high. We are actively
-  working on it. Use <strong>Knowledge</strong> or <strong>Board</strong> for
-  reliable browsing while we land the rewrite.
-  <button id="cortex-graph-warn-close" aria-label="Dismiss"
-          style="position:absolute;top:4px;right:6px;width:22px;height:22px;
-                 background:transparent;border:none;color:#FFB060;font-size:14px;
-                 cursor:pointer;line-height:1;padding:0">×</button>
-</div>
-<script>
-(function(){
-  var b = document.getElementById('cortex-graph-warn-close');
-  if (b) b.addEventListener('click', function() {
-    var w = document.getElementById('cortex-graph-warn');
-    if (w) w.style.display = 'none';
-  });
-})();
-</script>
-
 <div id="status-bar" class="hud-panel">
   <div class="status-dot"></div>
   <span id="status-text">Initializing</span>

ui/unified/js/controls.js

@@ -3,34 +3,23 @@
   document.addEventListener('DOMContentLoaded', function() {
     // ── View toggle (Graph / Timeline) ──
     var viewBtns = document.querySelectorAll('.view-toggle .view-btn[data-view]');
-    function _toggleGraphWarn(view) {
-      var w = document.getElementById('cortex-graph-warn');
-      if (!w) return;
-      // Show the experimental-graph banner only when the Graph tab is
-      // active. Other views hide it; the in-banner × button hides it
-      // permanently for the session.
-      if (view === 'graph') w.style.display = '';
-      else w.style.display = 'none';
-    }
     viewBtns.forEach(function(btn) {
       btn.addEventListener('click', function() {
-        // Disabled tabs (Pipeline) ignore clicks entirely.
-        if (btn.disabled || btn.hasAttribute('disabled')) return;
         viewBtns.forEach(function(b) { b.classList.remove('active'); });
         btn.classList.add('active');
-        var view = btn.dataset.view || 'knowledge';
+        var view = btn.dataset.view || 'graph';
         JUG.state.activeView = view;
         toggleFilterBarVisibility(view);
-        _toggleGraphWarn(view);
       });
     });
 
-    // Graph disabled. Knowledge is the landing tab — paged
-    // /api/memories scales to any N.
+    // Graph is the default landing view — the wiki is still under
+    // active restructuring and the workflow graph is the canonical
+    // answer to "what did Claude do in this project".
     setTimeout(function() {
       JUG.state.activeView = '_init';
-      JUG.state.activeView = 'knowledge';
-      toggleFilterBarVisibility('knowledge');
+      JUG.state.activeView = 'graph';
+      toggleFilterBarVisibility('graph');
     }, 0);
 
     // ── Filter buttons (source type) ──

ui/unified/js/polling.js

@@ -3,21 +3,11 @@
   var abortController = null;
 
   function fetchGraph() {
-    // Graph re-enabled (experimental). Knowledge is still the default
-    // landing tab so this fetch only matters once the user clicks the
-    // Graph tab — the warning banner above the view tells them what
-    // they're getting into. d3-force is gone (workflow_graph.js
-    // mounts a static-position renderer) but JSON.parse + buildGraph
-    // are still O(N+E) each and may freeze the browser at high N.
-    if (JUG.state && JUG.state.activeView !== 'graph') {
-      // Don't pay the cost unless the user actually wants the graph.
-      updateStatus('Online — graph standby');
-      hideLoading();
-      return;
-    }
     if (abortController) abortController.abort();
     abortController = new AbortController();
     var signal = abortController.signal;
+
+    // Single fetch — no batching. Domain dedup keeps node count manageable.
     fetch(JUG.API_URL, { signal: signal })
       .then(function(res) {
         if (!res.ok) throw new Error('HTTP ' + res.status);
@@ -144,9 +134,7 @@
       .map(function(v) { return String(v).padStart(2, '0'); }).join(':');
   }, 1000);
 
-  // Boot — delay initial fetch. fetchGraph() short-circuits when the
-  // Graph tab isn't active, so this is cheap on Knowledge / Board /
-  // Wiki landings.
+  // Boot — delay initial fetch to let Three.js scene fully initialize
   if (document.readyState === 'loading') {
     document.addEventListener('DOMContentLoaded', function() {
       setTimeout(fetchGraph, 500);
@@ -155,19 +143,8 @@
     setTimeout(fetchGraph, 500);
   }
 
-  // Trigger the heavy graph fetch only when the user actually
-  // switches to the Graph tab (lazy-load semantics).
-  if (window.JUG && JUG.on) {
-    JUG.on('state:activeView', function(ev) {
-      if (ev && ev.value === 'graph') setTimeout(fetchGraph, 50);
-    });
-  }
-
   function _loadDiscussionBatch(batch) {
-    // Discussion batches were merged into JUG.state.lastData — at high
-    // N this also accumulates hundreds of MB. Skip until we add a
-    // dedicated Discussions tab with its own paged path.
-    return;
+    var batchSize = 500;
     fetch(JUG.API_URL.replace('/api/graph', '/api/discussions') + '?batch=' + batch + '&batch_size=' + batchSize)
       .then(function(r) { return r.json(); })
       .then(function(data) {

ui/unified/js/state.js

@@ -17,7 +17,7 @@
     selectedId: null,
     zoomLevel: 'L0',
     lastData: null,
-    activeView: 'knowledge',
+    activeView: 'graph',
     domainFilter: '',
     emotionFilter: '',
     stageFilter: '',

ui/unified/js/workflow_graph.js

@@ -249,61 +249,28 @@
     //  * velocityDecay: 0.72 → 0.78       (ζ recovered to ~0.65)
     // Other force constants unchanged — slots from computeSlots carry
     // the positioning burden; physics just needs time to converge.
-    // ── d3-force simulation REMOVED ─────────────────────────────────
-    //
-    // The simulation was the dominant cost driver at high N: per tick
-    //    O(N log N) charge + O(E) link + O(N) collide + O(N) center
-    // = ~5M ops/tick × 60 fps = 300M ops/sec on the main thread for a
-    // 240k-node graph. Plus warmup 100 ticks + cooldown 400 ticks per
-    // mount. That's what froze the browser.
-    //
-    // Positions are now FINAL once `prepareTopology` has placed each
-    // node into its slot (slotOf[id]). The renderer paints once at
-    // those positions and stops — no tick loop, no continuous physics.
-    // Drag handlers move the node directly and call `renderer.refresh()`
-    // for a single repaint.
-    //
-    // We expose a `sim` shim so the existing renderers
-    // (workflow_graph_render_canvas.js / _svg.js) — which call
-    // `sim.on('tick', draw)`, `sim.alphaTarget(...).restart()` etc.
-    // for drag handling — keep working without modification.
-    nodes.forEach(function (n) {
-      var slot = ctx.slotOf && ctx.slotOf[n.id];
-      if (slot) { n.x = slot.x; n.y = slot.y; }
-      else if (n.x == null) { n.x = ctx.cx || width / 2; n.y = ctx.cy || height / 2; }
-    });
-    var _tickCb = function () {};
-    var sim = {
-      _nodes: nodes,
-      _scheduled: false,
-      nodes: function (n) { if (n) { this._nodes = n; } return this._nodes; },
-      force: function () { return sim; },     // no-op chainable
-      alpha: function () { return sim; },     // no-op chainable
-      alphaDecay: function () { return sim; },
-      alphaTarget: function () { return sim; },
-      velocityDecay: function () { return sim; },
-      restart: function () {
-        // Coalesce repaints to one per animation frame even under
-        // drag-storm — without this the SVG renderer redraws ~120
-        // times/sec while the user drags one node.
-        if (sim._scheduled) return sim;
-        sim._scheduled = true;
-        requestAnimationFrame(function () {
-          sim._scheduled = false;
-          try { _tickCb(); } catch (_) {}
-        });
-        return sim;
-      },
-      stop: function () { return sim; },
-      on: function (ev, cb) {
-        if (ev === 'tick' && typeof cb === 'function') {
-          _tickCb = cb;
-          // Single initial paint at the static slot positions.
-          try { cb(); } catch (_) {}
-        }
-        return sim;
-      },
-    };
+    var slotK    = HEAVY ? 1.2  : 0.85;
+    var chargeEn = true;
+    var collideI = HEAVY ? 2    : 3;
+    var alphaDK  = HEAVY ? 0.018 : 0.022;
+    var velDecay = 0.78;
+
+    var sim = d3.forceSimulation(nodes)
+      .alpha(1.0).alphaDecay(alphaDK).velocityDecay(velDecay)
+      .force('link', d3.forceLink(edges).id(function (n) { return n.id; })
+        .distance(linkDistance).strength(linkStrength))
+      .force('slot',        slotForce(ctx, slotK))
+      .force('interdomain', interDomainRepelForce(ctx, 0.08))
+      .force('symmulti', symbolMultiCenterForce(ctx))
+      .force('collide', d3.forceCollide()
+        .radius(function (n) { return collisionRadius(n, ctx); })
+        .strength(0.92).iterations(collideI));
+    if (chargeEn) {
+      // Local charge (distanceMax 180) so symbol-symbol repulsion
+      // doesn't create long-range feedback with the multi-centroid
+      // attraction; domains still repel each other via interdomain.
+      sim.force('charge', d3.forceManyBody().strength(chargeStrength).distanceMax(180));
+    }
 
     var useCanvas = nodes.length > CANVAS_THRESHOLD;
     var renderer = useCanvas
@@ -314,8 +281,7 @@
       var w = container.clientWidth || window.innerWidth;
       var h = container.clientHeight || window.innerHeight;
       renderer.resize(w, h);
-      // No simulation to restart — just repaint at the new viewport.
-      sim.restart();
+      sim.alpha(0.3).restart();
     }
     window.addEventListener('resize', onResize);