fix(hub): stop "Needs attention" items from perpetually reappearing

packages/codegraph/public/app.js

@@ -183,6 +183,12 @@ async function deprecateMemory(id) {
   else alert('Update failed')
 }
 
+async function reinforceMemory(id) {
+  const r = await fetch(`/api/memories/${encodeURIComponent(id)}/reinforce`, { method: 'POST' })
+  if (r.ok) { closeDetail(); route() }
+  else alert('Reinforce failed')
+}
+
 // ── Session actions ──
 async function cleanupDuplicates() {
   if (!confirm('Delete duplicate in-progress sessions (keeps most recent per project)?')) return
@@ -346,6 +352,7 @@ window.removeStackTag = removeStackTag
 window.addMemberRow = addMemberRow
 window.deleteMemory = deleteMemory
 window.deprecateMemory = deprecateMemory
+window.reinforceMemory = reinforceMemory
 window.cleanupDuplicates = cleanupDuplicates
 window.deleteSession = deleteSession
 window.loadEnvVars = loadEnvVars
@@ -436,8 +443,12 @@ window.applySkillUpdate = async (proposalId, btn) => {
 async function updateReviewBadge() {
   try {
     const data = await api.get('/api/review/pending')
-    const total = (data.memories?.length || 0) + (data.skills?.length || 0) +
-      (data.components?.length || 0) + (data.proposals?.length || 0) + (data.dsScans?.length || 0)
+    // Use the authoritative `totals` object, not array lengths: the memories query is
+    // LIMITed (default 100), so .length undercounts the badge once >100 are pending —
+    // exactly the backlog scenario. renderReview already uses data.totals; match it.
+    const t = data.totals || {}
+    const total = (t.memories || 0) + (t.skills || 0) +
+      (t.components || 0) + (t.proposals || 0) + (t.dsScans || 0)
     const badge = document.getElementById('review-badge')
     if (badge) {
       badge.textContent = total

packages/codegraph/public/js/render.js

@@ -71,6 +71,53 @@ function clearHubRefresh() {
   if (_hubVisibilityHandler) { document.removeEventListener('visibilitychange', _hubVisibilityHandler); _hubVisibilityHandler = null }
 }
 
+// Builds the "Needs attention" band HTML from the three counts. Shared by the
+// initial renderHome() and the 30s refreshHubLive() so the band stays in sync with
+// the adjacent System Health rows instead of freezing at its first-render value.
+function buildAttnBand(reviewTotal, decayCount, staleCount) {
+  const attnItems = []
+  if (reviewTotal > 0) attnItems.push({
+    count: reviewTotal,
+    label: reviewTotal === 1 ? 'Pending review' : 'Pending reviews',
+    hint: 'Approve or reject queued items',
+    target: '#/review',
+  })
+  if (decayCount > 0) attnItems.push({
+    count: decayCount,
+    label: decayCount === 1 ? 'Decaying memory' : 'Decaying memories',
+    hint: 'Confidence dropped through real decay',
+    target: '#/memories',
+  })
+  if (staleCount > 0) attnItems.push({
+    count: staleCount,
+    label: staleCount === 1 ? 'Stale memory' : 'Stale memories',
+    hint: 'Not updated in 90+ days',
+    target: '#/memories',
+  })
+  if (attnItems.length === 0) return ''
+  return `
+    <div class="hub-attention">
+      <div class="hub-attention-head">
+        <span class="hub-attention-icon">${HUB_ICONS.warn}</span>
+        Needs attention
+      </div>
+      ${attnItems.map(item => {
+        const sev = item.count <= 5 ? 'attn-warn' : 'attn-crit'
+        return `<div class="hub-attention-item ${sev}" tabindex="0" role="button"
+          aria-label="${item.label}: ${item.count}"
+          onclick="location.hash='${item.target}'" ${KEY_CLICK}>
+          <span class="attn-count">${item.count}</span>
+          <div class="attn-body">
+            <span class="attn-label">${item.label}</span>
+            <span class="attn-hint">${item.hint}</span>
+          </div>
+          <span class="attn-arrow">${HUB_ICONS.arrow}</span>
+        </div>`
+      }).join('')}
+    </div>
+  `
+}
+
 async function refreshHubLive() {
   const hash = location.hash || '#/'
   if (hash !== '#/' && hash !== '#' && hash !== '#/home') { clearHubRefresh(); return }
@@ -106,6 +153,33 @@ async function refreshHubLive() {
         dot.className = 'health-dot ' + (staleCount === 0 ? 'health-dot-ok' : staleCount <= 5 ? 'health-dot-warn' : 'health-dot-crit')
       }
     }
+    // Keep the "Needs attention" band in sync with the health rows. It was built once
+    // by renderHome and otherwise frozen, so it would diverge from the live "Pending
+    // reviews"/"Decay" rows (and never disappear when a count dropped to 0).
+    const freshBand = buildAttnBand(
+      reviewTotal,
+      typeof health.decayCount === 'number' ? health.decayCount : 0,
+      typeof health.staleCount === 'number' ? health.staleCount : 0,
+    )
+    const attnHost = document.querySelector('.hub-attention')
+    if (attnHost) {
+      if (freshBand) {
+        const tmp = document.createElement('template')
+        tmp.innerHTML = freshBand.trim()
+        attnHost.replaceWith(tmp.content.firstElementChild)
+      } else {
+        attnHost.remove()
+      }
+    } else if (freshBand) {
+      // Count went 0 -> >0 since first render: insert the band right after the greeting.
+      const greeting = document.querySelector('.hub-hero .hub-greeting-line')
+      if (greeting) {
+        const tmp = document.createElement('template')
+        tmp.innerHTML = freshBand.trim()
+        greeting.insertAdjacentElement('afterend', tmp.content.firstElementChild)
+      }
+    }
+
     const uptimeStrong = document.querySelector('.health-footer span:first-child strong')
     if (uptimeStrong) uptimeStrong.textContent = formatUptime(health.uptime || 0)
     const statusEl = document.getElementById('server-status')
@@ -277,7 +351,14 @@ export async function renderHome() {
   `).join('') || '<p style="color:var(--text-muted);font-size:12px">No memories yet.</p>'
 
   // ── System Health ──
-  const decayCount = health.decayCount ?? memories.filter(m => (m.confidence ?? 10) < 4).length
+  // Mirror the server predicate (http-server.ts computeAttentionCounts): a memory is
+  // "decaying" only if it actually aged (sessions_since_validation >= 5), not merely
+  // born below the confidence threshold. Excludes the M-_system_* metadata row.
+  const decayCount = health.decayCount ?? memories.filter(m =>
+    (m.confidence ?? 10) < 4 &&
+    (m.sessionsSinceValidation ?? 0) >= 5 &&
+    !(m.id || '').startsWith('M-_system_')
+  ).length
   const staleCount = health.staleCount ?? memories.filter(m => {
     const ts = m.updatedAt || m.updated_at || m.createdAt || m.created_at
     return ts && daysSince(ts) > 90
@@ -297,48 +378,8 @@ export async function renderHome() {
     ? `openProjectDetail('${escHtml(resumeProject)}')`
     : recentSession ? `location.hash='#/sessions'` : ''
 
-  // ── Attention band ──
-  const attnItems = []
-  if (reviewTotal > 0) attnItems.push({
-    count: reviewTotal,
-    label: reviewTotal === 1 ? 'Pending review' : 'Pending reviews',
-    hint: 'Approve or reject queued items',
-    target: '#/review',
-  })
-  if (decayCount > 0) attnItems.push({
-    count: decayCount,
-    label: decayCount === 1 ? 'Decaying memory' : 'Decaying memories',
-    hint: 'Confidence below 4',
-    target: '#/memories',
-  })
-  if (staleCount > 0) attnItems.push({
-    count: staleCount,
-    label: staleCount === 1 ? 'Stale memory' : 'Stale memories',
-    hint: 'Not updated in 90+ days',
-    target: '#/memories',
-  })
-
-  const attnBand = attnItems.length === 0 ? '' : `
-    <div class="hub-attention">
-      <div class="hub-attention-head">
-        <span class="hub-attention-icon">${HUB_ICONS.warn}</span>
-        Needs attention
-      </div>
-      ${attnItems.map(item => {
-        const sev = item.count <= 5 ? 'attn-warn' : 'attn-crit'
-        return `<div class="hub-attention-item ${sev}" tabindex="0" role="button"
-          aria-label="${item.label}: ${item.count}"
-          onclick="location.hash='${item.target}'" ${KEY_CLICK}>
-          <span class="attn-count">${item.count}</span>
-          <div class="attn-body">
-            <span class="attn-label">${item.label}</span>
-            <span class="attn-hint">${item.hint}</span>
-          </div>
-          <span class="attn-arrow">${HUB_ICONS.arrow}</span>
-        </div>`
-      }).join('')}
-    </div>
-  `
+  // ── Attention band ── (built via shared buildAttnBand so refreshHubLive can rebuild it)
+  const attnBand = buildAttnBand(reviewTotal, decayCount, staleCount)
 
   pageEl.innerHTML = `
     <section class="hub-hero">
@@ -404,7 +445,7 @@ export async function renderHome() {
           <div class="card-title">System health</div>
           <div class="health-row" data-health="decay" tabindex="0" role="button" aria-label="Decay alerts: ${decayCount}" onclick="location.hash='#/memories'" ${KEY_CLICK}>
             <span class="health-dot ${dotClass(decayCount)}"></span>
-            <span class="health-row-label">Decay alerts <span class="health-row-hint">(conf &lt; 4)</span></span>
+            <span class="health-row-label">Decay alerts <span class="health-row-hint">(conf &lt; 4 · aged)</span></span>
             <span class="health-row-val">${decayCount}</span>
           </div>
           <div class="health-row" data-health="review" tabindex="0" role="button" aria-label="Pending reviews: ${reviewTotal}" onclick="location.hash='#/review'" ${KEY_CLICK}>
@@ -767,6 +808,7 @@ export async function openMemoryDetail(id, openDetailFn) {
       <span style="color:var(--text-muted);font-size:11px;margin-left:8px">${m.skill || ''} &middot; ${m.scope}</span>
     </div>
     <div style="display:flex;gap:8px;margin-bottom:12px">
+      ${(m.confidence ?? 10) < 10 ? `<button onclick="reinforceMemory('${m.id}')" title="Confidence +1 and reset staleness — keep this memory healthy" style="padding:4px 12px;border-radius:6px;background:rgba(52,211,153,.1);border:1px solid var(--green);color:var(--green);font-size:11px;cursor:pointer">Reinforce</button>` : ''}
       <button onclick="deprecateMemory('${m.id}')" style="padding:4px 12px;border-radius:6px;background:rgba(245,158,11,.1);border:1px solid var(--yellow);color:var(--yellow);font-size:11px;cursor:pointer">Deprecate</button>
       <button onclick="deleteMemory('${m.id}')" style="padding:4px 12px;border-radius:6px;background:rgba(248,113,113,.1);border:1px solid var(--red);color:var(--red);font-size:11px;cursor:pointer">Delete</button>
     </div>

packages/codegraph/scripts/remediate-attention-backlog.sh

@@ -0,0 +1,117 @@
+#!/usr/bin/env bash
+#
+# Synapse — one-time remediation of the "Needs attention" backlog
+# (the historical 308 pending reviews / 30 decaying memories on production).
+#
+# Policy: AUTO-APPROVE IN-PLACE (chosen by the operator). It drains the
+# auto-generated review backlog without manual triage:
+#   - pending-review memories            -> active, staleness reset
+#   - all active memories with ssv >= 5  -> staleness reset (clean slate; the
+#                                           kept auto-enqueue restarts its 15-cycle clock)
+#   - pending skill_proposals            -> dismissed (auto-generated nudges)
+#   - pending design_system_scans        -> dismissed (auto-generated)
+#   - decay metadata clock               -> reset to now
+#
+# IMPORTANT — run order:
+#   1. Deploy the new code FIRST so migration 034 (dedup indexes) has run and the
+#      new approve/decay logic is live. Otherwise the backlog will simply refill.
+#   2. Then run this script on the box that holds the production DB (Coolify container).
+#
+# It refuses to run without a backup and prints before/after counts.
+#
+# Usage:
+#   ./remediate-attention-backlog.sh [/path/to/graph.db]
+# Default DB path: /data/.codegraph/graph.db   (Synapse production layout)
+
+set -euo pipefail
+
+DB="${1:-/data/.codegraph/graph.db}"
+
+if ! command -v sqlite3 >/dev/null 2>&1; then
+  echo "ERROR: sqlite3 not found in PATH." >&2
+  exit 1
+fi
+if [[ ! -f "$DB" ]]; then
+  echo "ERROR: database not found at: $DB" >&2
+  echo "Pass the correct path as the first argument." >&2
+  exit 1
+fi
+
+STAMP="$(date +%Y%m%d-%H%M%S)"
+BACKUP="${DB}.bak-pre-attention-remediation-${STAMP}"
+
+echo "==> Database:  $DB"
+echo "==> Backup:    $BACKUP"
+# .backup is safe on a live WAL DB (consistent snapshot).
+sqlite3 "$DB" ".backup '$BACKUP'"
+echo "==> Backup created."
+
+echo
+echo "==> BEFORE:"
+sqlite3 "$DB" <<'SQL'
+.mode column
+.headers on
+SELECT 'memories.pending-review' AS metric, COUNT(*) AS n FROM memories WHERE status='pending-review'
+UNION ALL SELECT 'memories.active.ssv>=15', COUNT(*) FROM memories WHERE status='active' AND sessions_since_validation>=15
+UNION ALL SELECT 'decaying(real: conf<4 & ssv>=5)', COUNT(*) FROM memories WHERE status='active' AND confidence<4 AND sessions_since_validation>=5 AND id NOT LIKE 'M-_system_%'
+UNION ALL SELECT 'skill_proposals.pending', COUNT(*) FROM skill_proposals WHERE status='pending'
+UNION ALL SELECT 'design_system_scans.pending', COUNT(*) FROM design_system_scans WHERE status='pending';
+SQL
+
+echo
+echo "==> Applying remediation (single transaction)…"
+sqlite3 "$DB" <<'SQL'
+BEGIN;
+
+-- 1. Auto-approve every queued memory in place + reset its staleness so the next
+--    decay cycle does not immediately re-flag it (these were timer-generated, not
+--    human-queued).
+UPDATE memories
+   SET status = 'active',
+       sessions_since_validation = 0,
+       last_validated = strftime('%Y-%m-%dT%H:%M:%fZ','now'),
+       updated_at     = strftime('%Y-%m-%dT%H:%M:%fZ','now')
+ WHERE status = 'pending-review';
+
+-- 2. Clean slate for the kept auto-enqueue mechanism: reset the staleness clock on
+--    every active memory that had already aged, so the 15-cycle countdown restarts
+--    fresh after the fix instead of immediately re-queuing a wave of old memories.
+UPDATE memories
+   SET sessions_since_validation = 0,
+       updated_at = strftime('%Y-%m-%dT%H:%M:%fZ','now')
+ WHERE status = 'active'
+   AND sessions_since_validation >= 5
+   AND id NOT LIKE 'M-_system_%';
+
+-- 3. Dismiss the auto-generated proposal/scan nudges (content is untouched; they
+--    re-propose only when genuinely warranted now that dedup indexes exist).
+UPDATE skill_proposals      SET status = 'dismissed', reviewed_at = strftime('%Y-%m-%dT%H:%M:%fZ','now') WHERE status = 'pending';
+UPDATE design_system_scans  SET status = 'dismissed' WHERE status = 'pending';
+
+-- 4. Reset the decay clock so the next scheduler tick starts a fresh 24h window.
+UPDATE memories SET updated_at = strftime('%Y-%m-%dT%H:%M:%fZ','now') WHERE id = 'M-_system_decay_last_run';
+
+COMMIT;
+SQL
+
+echo "==> Done."
+echo
+echo "==> AFTER:"
+sqlite3 "$DB" <<'SQL'
+.mode column
+.headers on
+SELECT 'memories.pending-review' AS metric, COUNT(*) AS n FROM memories WHERE status='pending-review'
+UNION ALL SELECT 'memories.active.ssv>=15', COUNT(*) FROM memories WHERE status='active' AND sessions_since_validation>=15
+UNION ALL SELECT 'decaying(real: conf<4 & ssv>=5)', COUNT(*) FROM memories WHERE status='active' AND confidence<4 AND sessions_since_validation>=5 AND id NOT LIKE 'M-_system_%'
+UNION ALL SELECT 'skill_proposals.pending', COUNT(*) FROM skill_proposals WHERE status='pending'
+UNION ALL SELECT 'design_system_scans.pending', COUNT(*) FROM design_system_scans WHERE status='pending';
+SQL
+
+echo
+echo "All five counters should now read 0. If anything looks wrong, restore with:"
+echo "    cp '$BACKUP' '$DB'   # (stop the server first)"
+echo
+echo "NOTE: pending skill/component DRAFTS (skills.status='pending' / ui_components.status='pending')"
+echo "are intentional human/agent submissions and are NOT auto-approved here. Review them in the"
+echo "dashboard, or to also auto-approve them (publishes unreviewed drafts) run:"
+echo "    sqlite3 '$DB' \"UPDATE skills SET status='active' WHERE status='pending'; UPDATE ui_components SET status='active' WHERE status='pending';\""

packages/codegraph/src/mcp/http-server.ts

@@ -164,8 +164,20 @@ export function computeAttentionCounts(db: import('better-sqlite3').Database): {
 } {
   const staleCutoff = new Date(Date.now() - STALE_DAYS * 24 * 60 * 60 * 1000).toISOString()
 
+  // "Decaying" must mean a memory that has ACTUALLY decayed — not one merely born
+  // below the threshold. New memories are created with low confidence (default 1),
+  // and applyDecay only lowers confidence once sessions_since_validation >= 5, so the
+  // bare `confidence < 4` predicate counted every fresh/unvalidated memory as
+  // "decaying" — definitional noise that could never be cleared. Requiring
+  // ssv >= 5 means the row went through >=5 unvalidated decay cycles. The system
+  // metadata row (M-_system_*) is excluded for parity with allActive().
   const decayCount = (db.prepare(
-    `SELECT COUNT(*) AS n FROM memories WHERE status = 'active' AND confidence IS NOT NULL AND confidence < 4`
+    `SELECT COUNT(*) AS n FROM memories
+      WHERE status = 'active'
+        AND confidence IS NOT NULL
+        AND confidence < 4
+        AND sessions_since_validation >= 5
+        AND id NOT LIKE 'M-_system_%'`
   ).get() as { n: number }).n
 
   const staleCount = (db.prepare(

packages/codegraph/src/mcp/routes/memories.ts

@@ -116,5 +116,23 @@ export function createMemoriesRouter(ctx: RouteContext): Router {
     }
   })
 
+  // Non-destructive "Reinforce / Keep" action: bumps confidence +1 and resets the
+  // staleness counter so a valuable low-confidence memory can be rehabilitated from
+  // the dashboard instead of only Deprecate/Delete. Also doubles as the human
+  // counterpart to the auto-decay's pending-review flagging.
+  router.post('/api/memories/:id/reinforce', (req, res) => {
+    const userId = (req as any).userId as string | undefined
+    try {
+      const db = openDb(ctx.skillbrainRoot)
+      const store = new MemoryStore(db)
+      const ok = store.reinforce(req.params.id, userId)
+      closeDb(db)
+      if (!ok) { res.status(404).json({ error: 'Memory not found' }); return }
+      res.json({ ok: true })
+    } catch (err: any) {
+      res.status(500).json({ error: err.message })
+    }
+  })
+
   return router
 }

packages/codegraph/src/mcp/routes/review.ts

@@ -60,8 +60,15 @@ export function createReviewRouter(ctx: RouteContext): Router {
   router.post('/api/review/memory/:id/approve', (req, res) => {
     const db = openDb(ctx.skillbrainRoot)
     const now = new Date().toISOString()
-    db.prepare(`UPDATE memories SET status = 'active', updated_at = ? WHERE id = ?`)
-      .run(now, req.params.id)
+    // Reset the staleness counter on approve. A memory lands in 'pending-review'
+    // because markPendingReview fired (sessions_since_validation >= 15). If we only
+    // flip status back to 'active', the very next 24h decay cycle increments ssv and
+    // markPendingReview re-flags it — so the approval never sticks and the queue never
+    // drains. Treating a human approval as a validation event (ssv=0 + last_validated)
+    // mirrors reinforceMemory, minus the confidence bump (approve = "leave it", not
+    // "this proved useful"). The memory must now age 15 fresh cycles before re-queuing.
+    db.prepare(`UPDATE memories SET status = 'active', sessions_since_validation = 0, last_validated = ?, updated_at = ? WHERE id = ?`)
+      .run(now, now, req.params.id)
     new AuditStore(db).log({ entityType: 'memory', entityId: req.params.id, action: 'approve', reviewedBy: (req as any).userId ?? 'unknown' })
     closeDb(db)
     res.json({ ok: true })