claude-code-memory-explorer 0.2.5 → 0.3.0

package/README.md

@@ -62,6 +62,7 @@ Claude Code stores memory across multiple locations:
 | CLAUDE.local.md | `./CLAUDE.local.md` | Always |
 | Rules | `.claude/rules/*.md` | Conditional (path-scoped) |
 | Auto memory | `~/.claude/projects/<encoded>/memory/` | Startup (MEMORY.md) or on-demand |
+| Agent memory | `~/.claude/agent-memory/<agent>/`, `./.claude/agent-memory/<agent>/`, `./.claude/agent-memory-local/<agent>/` | Startup (MEMORY.md) or on-demand |
 
 The dashboard:
 1. **Scans** all memory locations — `~/.claude/`, ancestor directories, project rules, auto memory

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "claude-code-memory-explorer",
-  "version": "0.2.5",
+  "version": "0.3.0",
   "description": "Memory explorer dashboard for Claude Code",
   "main": "server.js",
   "bin": {

package/public/app.js

@@ -243,14 +243,14 @@ function bindModalKeys(inputId, modalId, submitFn) {
 
 // #region RENDER_TREE
 
-const SCOPE_ORDER = ['policy', 'user', 'user-memory', 'project', 'rule', 'memory'];
+const SCOPE_ORDER = ['policy', 'user', 'project', 'rule', 'memory', 'agent-memory'];
 const SCOPE_LABELS = {
   policy: 'Managed Policy',
-  'user-memory': 'User Memory',
   user: 'User',
   project: 'Project',
   rule: 'Rules',
   memory: 'Auto Memory',
+  'agent-memory': 'Agent Memory',
 };
 const LOAD_ICONS = {
   always: '\u25CF',
@@ -317,7 +317,8 @@ function renderTree() {
     const meta = `${item.lines}L`;
     const isConditional = item.load === 'conditional' || item.load === 'ondemand';
     const pad = indent ? ` style="padding-left:${12 + indent * 16}px"` : '';
-    let h = `<div class="tree-item${sel}${indent ? ' tree-child' : ''}${isConditional ? ' tree-conditional' : ''}" data-id="${esc(item.id)}" title="${esc(item.path)}" onclick="selectFile('${escJs(item.id)}')"${pad}>`;
+    const muted = item.scope === 'agent-memory' ? ' tree-agent-item' : '';
+    let h = `<div class="tree-item${sel}${indent ? ' tree-child' : ''}${isConditional ? ' tree-conditional' : ''}${muted}" data-id="${esc(item.id)}" title="${esc(item.path)}" onclick="selectFile('${escJs(item.id)}')"${pad}>`;
     h += `<span class="load-icon" title="${loadTitle}" style="color:var(--scope-${item.scope})">${loadIcon}</span>`;
     h += `<span class="file-name">${esc(item.name)}</span>`;
     h += `<span class="file-meta">${meta}</span>`;
@@ -334,12 +335,67 @@ function renderTree() {
     const items = groups[scope];
     if (!items) continue;
     const label = SCOPE_LABELS[scope] || scope;
-    html += `<div class="tree-group-header"><span class="scope-dot" style="color:var(--scope-${scope})">\u25CF</span> ${esc(label)} <span style="opacity:0.5">${items.length}</span></div>`;
-    for (const item of items) html += renderItem(item, 0);
+    const collapsible = scope === 'agent-memory';
+    const collapsed = collapsible && isGroupCollapsed(scope);
+    const chevron = collapsible ? `<span class="group-chevron">${collapsed ? '\u25B8' : '\u25BE'}</span>` : '';
+    const headerClass = collapsible ? 'tree-group-header tree-group-clickable' : 'tree-group-header';
+    const onclick = collapsible ? ` onclick="_toggleGroup('${escJs(scope)}')"` : '';
+    html += `<div class="${headerClass}" data-scope="${esc(scope)}"${onclick}>${chevron}<span class="scope-dot" style="color:var(--scope-${scope})">\u25CF</span> ${esc(label)} <span style="opacity:0.5">${items.length}</span></div>`;
+    if (collapsed) continue;
+    if (scope === 'agent-memory') {
+      const sorted = [...items].sort((a, b) => {
+        const so = ['user', 'project', 'local'];
+        return (
+          so.indexOf(a.agentScope) - so.indexOf(b.agentScope) ||
+          a.agentName.localeCompare(b.agentName) ||
+          (a.name === 'MEMORY.md' ? -1 : 1)
+        );
+      });
+      let lastKey = null;
+      for (const item of sorted) {
+        const key = `${item.agentScope}/${item.agentName}`;
+        if (key !== lastKey) {
+          html += `<div class="tree-subgroup-header" title="${esc(item.agentScope)} scope"><span class="agent-name">${esc(item.agentName)}</span><span class="agent-scope-tag">${esc(item.agentScope)}</span></div>`;
+          lastKey = key;
+        }
+        html += renderItem(item, 1);
+      }
+    } else {
+      for (const item of items) html += renderItem(item, 0);
+    }
   }
   container.innerHTML = html;
 }
 
+const COLLAPSED_DEFAULTS = ['agent-memory'];
+function getCollapsedGroups() {
+  try {
+    const stored = localStorage.getItem('collapsedGroups');
+    if (stored !== null) return new Set(JSON.parse(stored));
+  } catch {}
+  return new Set(COLLAPSED_DEFAULTS);
+}
+function isGroupCollapsed(scope) {
+  return getCollapsedGroups().has(scope);
+}
+function setGroupCollapsed(scope, collapsed) {
+  const set = getCollapsedGroups();
+  if (collapsed) set.add(scope);
+  else set.delete(scope);
+  localStorage.setItem('collapsedGroups', JSON.stringify([...set]));
+}
+function _toggleGroup(scope) {
+  setGroupCollapsed(scope, !isGroupCollapsed(scope));
+  renderTree();
+}
+function getItemScope(item) {
+  return item?.parentId ? stackData.find((s) => s.id === item.parentId)?.scope : item?.scope;
+}
+function expandGroupForItem(item) {
+  const scope = getItemScope(item);
+  if (scope && isGroupCollapsed(scope)) setGroupCollapsed(scope, false);
+}
+
 function pushFileState(id) {
   const url = id ? `#${encodeURIComponent(id)}` : location.pathname;
   history.pushState({ fileId: id }, '', url);
@@ -368,7 +424,9 @@ function navigateTree(direction) {
     if (idx < 0) idx = navOrder.length - 1;
     if (idx >= navOrder.length) idx = 0;
   }
-  selectedFileId = navOrder[idx].id;
+  const target = navOrder[idx];
+  selectedFileId = target.id;
+  expandGroupForItem(target);
   pushFileState(selectedFileId);
   renderTree();
   renderPreview();
@@ -381,8 +439,7 @@ function navigateGroup(direction) {
   if (!activeScopes.length) return;
 
   const current = stackData.find((s) => s.id === selectedFileId);
-  const currentScope = current?.parentId ? stackData.find((s) => s.id === current.parentId)?.scope : current?.scope;
-  let scopeIdx = activeScopes.indexOf(currentScope);
+  let scopeIdx = activeScopes.indexOf(getItemScope(current));
   if (scopeIdx === -1) {
     scopeIdx = direction > 0 ? 0 : activeScopes.length - 1;
   } else {
@@ -390,7 +447,9 @@ function navigateGroup(direction) {
     if (scopeIdx < 0) scopeIdx = activeScopes.length - 1;
     if (scopeIdx >= activeScopes.length) scopeIdx = 0;
   }
-  selectedFileId = groups[activeScopes[scopeIdx]][0].id;
+  const target = groups[activeScopes[scopeIdx]][0];
+  selectedFileId = target.id;
+  expandGroupForItem(target);
   pushFileState(selectedFileId);
   renderTree();
   renderPreview();
@@ -401,6 +460,10 @@ function navigateGroup(direction) {
 
 // #region MEMORY_INDEX
 
+function isMemoryIndex(source) {
+  return (source.scope === 'memory' || source.scope === 'agent-memory') && source.name === 'MEMORY.md';
+}
+
 function parseMemoryIndex(content) {
   const entries = [];
   for (const line of content.split('\n')) {
@@ -458,6 +521,12 @@ async function renderPreview() {
   html += `<span class="scope-badge scope-${source.scope}">${esc(source.scope)}</span>`;
   html += `<span class="file-path">${esc(source.name)}</span>`;
   html += '<div class="preview-actions">';
+  if (isMemoryIndex(source)) {
+    const broken = (source.unresolvedImports || []).length;
+    if (broken) {
+      html += `<button class="action-btn small" onclick="_cleanupOrphans('${escJs(source.path)}')" title="Cleanup ${broken} orphaned refs"><svg width="12" height="12" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round"><path d="M3 6h18"/><path d="M8 6V4a2 2 0 0 1 2-2h4a2 2 0 0 1 2 2v2"/><path d="M19 6l-1 14a2 2 0 0 1-2 2H8a2 2 0 0 1-2-2L5 6"/><path d="M12 11v6"/></svg><span style="margin-left:3px">${broken}</span></button>`;
+    }
+  }
   html += `<button class="action-btn small" onclick="openInEditor('${escJs(source.path)}')" title="Open in VS Code"><svg width="12" height="12" viewBox="0 0 24 24" fill="currentColor" stroke="none"><path d="M17.583 2.207a1.1 1.1 0 0 1 1.541.033l2.636 2.636a1.1 1.1 0 0 1 .033 1.541L10.68 17.53a1.1 1.1 0 0 1-.345.247l-4.56 1.903a.55.55 0 0 1-.725-.725l1.903-4.56a1.1 1.1 0 0 1 .247-.345zm.902 1.87-8.794 8.793-.946 2.268 2.268-.946 8.794-8.793z"/></svg></button>`;
   html += `<button class="action-btn small" onclick="_confirmDeleteFile('${escJs(source.path)}','${escJs(source.name)}')" title="Delete file"><svg width="12" height="12" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round"><polyline points="3 6 5 6 21 6"/><path d="M19 6l-1 14a2 2 0 0 1-2 2H8a2 2 0 0 1-2-2L5 6"/><path d="M10 11v6M14 11v6"/><path d="M9 6V4a1 1 0 0 1 1-1h4a1 1 0 0 1 1 1v2"/></svg></button>`;
   html += '</div></div>';
@@ -474,10 +543,13 @@ async function renderPreview() {
   }
   html += '</div>';
 
-  // Imports — only show children (files that have this source as parent)
+  const content = fileData.content || '';
+  const memoryEntries = isMemoryIndex(source) ? parseMemoryIndex(content) : [];
+  const showMemoryTable = memoryEntries.length > 0;
+
   const children = stackData.filter((s) => s.parentId === source.id);
   const unresolved = source.unresolvedImports || [];
-  if (children.length || unresolved.length) {
+  if (!showMemoryTable && (children.length || unresolved.length)) {
     html += '<div class="preview-imports">';
     for (const child of children) {
       html += `<a class="import-link" href="#" onclick="selectFile('${escJs(child.id)}');return false" title="${esc(child.path)}">${esc(child.name)}</a>`;
@@ -493,22 +565,19 @@ async function renderPreview() {
   // File path
   html += `<div class="preview-filepath">${esc(source.path)}</div>`;
 
-  // Content — with cutoff line for auto memory startup files
-  const content = fileData.content || '';
   const hl = (text) => {
     const { text: processed, placeholders } = linkifyImports(text, source.id);
     return restorePlaceholders(highlightSource(processed, source.name), placeholders);
   };
 
-  // Memory index view — render structured table for MEMORY.md index files
-  if ((source.scope === 'memory' || source.scope === 'user-memory') && source.name === 'MEMORY.md') {
-    const entries = parseMemoryIndex(content);
-    if (entries.length) {
-      html += renderMemoryIndexTable(entries);
-    }
+  if (showMemoryTable) {
+    html += renderMemoryIndexTable(memoryEntries);
+    html += `<pre class="preview-code"><code>${hl(content)}</code></pre>`;
+    panel.innerHTML = html;
+    return;
   }
 
-  if ((source.scope === 'memory' || source.scope === 'user-memory') && source.load === 'startup' && source.maxLines) {
+  if ((source.scope === 'memory' || source.scope === 'agent-memory') && source.load === 'startup' && source.maxLines) {
     const lines = content.split('\n');
     const cutoff = source.maxLines;
     if (lines.length > cutoff) {
@@ -574,6 +643,54 @@ async function _submitDeleteFile() {
   }
 }
 
+function _cleanupOrphans(filePath) {
+  const source = stackData.find((s) => s.path === filePath);
+  const broken = source?.unresolvedImports || [];
+  if (!broken.length) {
+    showToast('No orphaned refs', 'info');
+    return;
+  }
+  const modal = document.getElementById('cleanupOrphansModal');
+  modal.dataset.filePath = filePath;
+  document.getElementById('cleanupOrphansCount').textContent = broken.length;
+  document.getElementById('cleanupOrphansList').innerHTML = broken.map((r) => `<li>${esc(r)}</li>`).join('');
+  modal.classList.add('open');
+}
+
+async function _submitCleanupOrphans() {
+  const modal = document.getElementById('cleanupOrphansModal');
+  const filePath = modal.dataset.filePath;
+  if (!filePath) return;
+  const btn = document.getElementById('cleanupOrphansSubmit');
+  btn.disabled = true;
+  btn.textContent = 'Cleaning...';
+  try {
+    const res = await fetch('/api/memory/cleanup-orphans', {
+      method: 'POST',
+      headers: { 'Content-Type': 'application/json' },
+      body: JSON.stringify({ path: filePath }),
+    });
+    if (!res.ok) {
+      const msg = await res
+        .json()
+        .then((e) => e.error)
+        .catch(() => `Cleanup failed (${res.status})`);
+      showToast(msg, 'error');
+      return;
+    }
+    const data = await res.json();
+    closeModal('cleanupOrphansModal');
+    delete modal.dataset.filePath;
+    await loadData();
+    showToast(`Removed ${data.removed.length} orphaned ref${data.removed.length === 1 ? '' : 's'}`, 'success');
+  } catch (err) {
+    showToast(err.message, 'error');
+  } finally {
+    btn.disabled = false;
+    btn.textContent = 'Remove';
+  }
+}
+
 async function openInEditor(filePath) {
   showToast('Opening...', 'info');
   try {

package/public/index.html

@@ -34,12 +34,12 @@
     <button class="topbar-btn" id="refreshBtn" title="Refresh (r)" onclick="refreshData()">
       <svg width="14" height="14" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2"><polyline points="23 4 23 10 17 10"/><path d="M20.49 15a9 9 0 11-2.12-9.36L23 10"/></svg>
     </button>
-    <button class="topbar-btn" id="helpBtn" title="Keyboard shortcuts (?)" onclick="toggleHelpModal()">
-      <svg width="14" height="14" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2"><circle cx="12" cy="12" r="10"/><path d="M9.09 9a3 3 0 0 1 5.83 1c0 2-3 3-3 3"/><circle cx="12" cy="17" r="0.5" fill="currentColor"/></svg>
-    </button>
     <button class="topbar-btn" id="themeBtn" title="Toggle theme (t)" onclick="toggleTheme()">
       <svg width="14" height="14" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2"><circle cx="12" cy="12" r="5"/><line x1="12" y1="1" x2="12" y2="3"/><line x1="12" y1="21" x2="12" y2="23"/><line x1="4.22" y1="4.22" x2="5.64" y2="5.64"/><line x1="18.36" y1="18.36" x2="19.78" y2="19.78"/><line x1="1" y1="12" x2="3" y2="12"/><line x1="21" y1="12" x2="23" y2="12"/><line x1="4.22" y1="19.78" x2="5.64" y2="18.36"/><line x1="18.36" y1="5.64" x2="19.78" y2="4.22"/></svg>
     </button>
+    <button class="topbar-btn" id="helpBtn" title="Keyboard shortcuts (?)" onclick="toggleHelpModal()">
+      <svg width="14" height="14" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2"><circle cx="12" cy="12" r="10"/><path d="M9.09 9a3 3 0 0 1 5.83 1c0 2-3 3-3 3"/><circle cx="12" cy="17" r="0.5" fill="currentColor"/></svg>
+    </button>
     <a class="topbar-btn" href="https://github.com/NikiforovAll/claude-code-memory" target="_blank" rel="noopener" title="GitHub">
       <svg width="16" height="16" viewBox="0 0 24 24" fill="currentColor" stroke="none"><path d="M12 0C5.37 0 0 5.37 0 12c0 5.31 3.435 9.795 8.205 11.385.6.105.825-.255.825-.57 0-.285-.015-1.23-.015-2.235-3.015.555-3.795-.735-4.035-1.41-.135-.345-.72-1.41-1.23-1.695-.42-.225-1.02-.78-.015-.795.945-.015 1.62.87 1.845 1.23 1.08 1.815 2.805 1.305 3.495.99.105-.78.42-1.305.765-1.605-2.67-.3-5.46-1.335-5.46-5.925 0-1.305.465-2.385 1.23-3.225-.12-.3-.54-1.53.12-3.18 0 0 1.005-.315 3.3 1.23.96-.27 1.98-.405 3-.405s2.04.135 3 .405c2.295-1.56 3.3-1.23 3.3-1.23.66 1.65.24 2.88.12 3.18.765.84 1.23 1.905 1.23 3.225 0 4.605-2.805 5.625-5.475 5.925.435.375.81 1.095.81 2.22 0 1.605-.015 2.895-.015 3.3 0 .315.225.69.825.57A12.02 12.02 0 0024 12c0-6.63-5.37-12-12-12z"/></svg>
     </a>
@@ -122,6 +122,24 @@
     </div>
   </div>
 
+  <!-- Cleanup orphans modal -->
+  <div class="modal-overlay" id="cleanupOrphansModal" onclick="if(event.target===this)closeModal('cleanupOrphansModal')">
+    <div class="modal">
+      <div class="modal-header">
+        <h3>Cleanup orphaned refs?</h3>
+        <button class="modal-close" onclick="closeModal('cleanupOrphansModal')">&#10005;</button>
+      </div>
+      <div class="modal-body">
+        <p class="modal-desc">Remove <strong id="cleanupOrphansCount"></strong> bullet line(s) from MEMORY.md that point to files missing on disk.</p>
+        <ul id="cleanupOrphansList" class="modal-orphan-list"></ul>
+        <div class="modal-actions">
+          <button class="action-btn" onclick="closeModal('cleanupOrphansModal')">Cancel</button>
+          <button class="action-btn danger" id="cleanupOrphansSubmit" onclick="_submitCleanupOrphans()">Remove</button>
+        </div>
+      </div>
+    </div>
+  </div>
+
   <!-- Help modal -->
   <div class="modal-overlay" id="helpModal" onclick="if(event.target===this)toggleHelpModal()">
     <div class="modal">

package/public/style.css

@@ -24,7 +24,7 @@
   --scope-local: #8a9bb5;
   --scope-rule: #a89bc4;
   --scope-memory: #c4a06a;
-  --scope-user-memory: #9ab87a;
+  --scope-agent-memory: #8aa8a3;
   --scope-policy: #b58a8a;
   --font-mono: 'IBM Plex Mono', monospace;
   --font-serif: 'Playfair Display', serif;
@@ -261,6 +261,49 @@ body {
   align-items: center;
   gap: 6px;
 }
+.tree-subgroup-header {
+  padding: 6px 12px 2px 20px;
+  font-size: 11px;
+  font-family: var(--font-mono);
+  color: var(--text-muted);
+  display: flex;
+  align-items: center;
+  gap: 8px;
+  opacity: 0.85;
+}
+.tree-subgroup-header .agent-name {
+  color: var(--text-tertiary);
+}
+.tree-subgroup-header .agent-scope-tag {
+  font-size: 9px;
+  font-weight: 600;
+  text-transform: uppercase;
+  letter-spacing: 0.4px;
+  padding: 1px 5px;
+  border-radius: 3px;
+  background: rgba(138, 168, 163, 0.12);
+  color: var(--scope-agent-memory);
+  opacity: 0.85;
+}
+.tree-group-clickable {
+  cursor: pointer;
+  user-select: none;
+}
+.tree-group-clickable:hover {
+  color: var(--text-secondary);
+}
+.group-chevron {
+  display: inline-block;
+  width: 10px;
+  font-size: 9px;
+  color: var(--text-muted);
+}
+.tree-agent-item .file-name {
+  opacity: 0.7;
+}
+body.light .tree-agent-item .file-name {
+  opacity: 0.8;
+}
 .tree-item {
   padding: 5px 12px 5px 24px;
   cursor: pointer;
@@ -411,20 +454,27 @@ body.light .tree-conditional .file-name {
 }
 .memory-index-row {
   display: grid;
-  grid-template-columns: 72px 160px 1fr;
+  grid-template-columns: 72px max-content 1fr;
   align-items: baseline;
   gap: 8px;
   padding: 3px 0;
 }
 .memory-index-type {
-  flex-shrink: 0;
+  text-align: center;
+  justify-self: center;
+}
+.modal-orphan-list {
+  margin: 0;
+  padding: 8px 12px 8px 28px;
+  list-style: disc;
+  font-family: var(--font-mono);
+  font-size: 11px;
+  color: var(--text-muted);
 }
 .memory-index-name {
   font-size: 11px;
   font-family: var(--font-mono);
   white-space: nowrap;
-  overflow: hidden;
-  text-overflow: ellipsis;
 }
 .memory-index-desc {
   font-size: 10px;
@@ -484,9 +534,9 @@ body.light .tree-conditional .file-name {
   background: rgba(196, 149, 106, 0.18);
   color: var(--scope-memory);
 }
-.scope-user-memory {
-  background: rgba(154, 184, 122, 0.18);
-  color: var(--scope-user-memory);
+.scope-agent-memory {
+  background: rgba(138, 168, 163, 0.18);
+  color: var(--scope-agent-memory);
 }
 .scope-policy {
   background: rgba(181, 138, 138, 0.18);

package/server.js

@@ -52,6 +52,10 @@ function clearCache() {
 
 // #region FILESYSTEM_SCANNING
 
+const CLAUDE_MD_VARIANTS = ['CLAUDE.md', '.claude/CLAUDE.md', 'CLAUDE.local.md', '.claude/CLAUDE.local.md'];
+
+const slug = s => s.replace(/[^a-zA-Z0-9]/g, '-');
+
 const MANAGED_POLICY_PATHS = process.platform === 'win32'
   ? [path.join(process.env.ProgramFiles || 'C:\\Program Files', 'ClaudeCode', 'CLAUDE.md')]
   : process.platform === 'darwin'
@@ -160,6 +164,11 @@ function spreadImports(filePath, content) {
   return { imports: resolved, softImports: resolvedSoft, unresolvedImports: unresolved };
 }
 
+function hasPathsFilter(frontmatter) {
+  if (!frontmatter || !frontmatter.paths) return false;
+  return Array.isArray(frontmatter.paths) ? frontmatter.paths.length > 0 : true;
+}
+
 function discoverMemorySources(projectPath) {
   const sources = [];
 
@@ -202,7 +211,7 @@ function discoverMemorySources(projectPath) {
         id: `user-rule-${path.basename(file, '.md')}`,
         name: path.basename(file),
         scope: 'rule',
-        load: 'conditional',
+        load: hasPathsFilter(info.frontmatter) ? 'conditional' : 'always',
         ...info,
         ruleSource: 'user',
         ...spreadImports(info.path, info.content),
@@ -214,16 +223,16 @@ function discoverMemorySources(projectPath) {
   const ancestors = getAncestorDirs(projectPath);
   const seenPaths = new Set(sources.map(s => s.path));
   for (const dir of ancestors) {
-    for (const name of ['CLAUDE.md', '.claude/CLAUDE.md']) {
-      const filePath = path.join(dir, name);
+    const isProjectRoot = path.resolve(dir) === path.resolve(projectPath);
+    for (const rel of CLAUDE_MD_VARIANTS) {
+      const filePath = path.join(dir, rel);
       if (seenPaths.has(filePath)) continue;
       const info = fileInfo(filePath);
       if (!info) continue;
       seenPaths.add(filePath);
-      const isProjectRoot = path.resolve(dir) === path.resolve(projectPath);
       sources.push({
-        id: `project-claude-md-${dir.replace(/[^a-zA-Z0-9]/g, '-')}`,
-        name: name.includes('/') ? '.claude/CLAUDE.md' : 'CLAUDE.md',
+        id: `project-claude-md-${slug(rel)}-${slug(dir)}`,
+        name: rel,
         scope: 'project',
         load: 'always',
         ...info,
@@ -231,23 +240,6 @@ function discoverMemorySources(projectPath) {
         isProjectRoot,
         ...spreadImports(info.path, info.content),
       });
-      break;
-    }
-
-    const localPath = path.join(dir, 'CLAUDE.local.md');
-    if (seenPaths.has(localPath)) continue;
-    const localInfo = fileInfo(localPath);
-    if (localInfo) {
-      seenPaths.add(localPath);
-      sources.push({
-        id: `local-claude-md-${dir.replace(/[^a-zA-Z0-9]/g, '-')}`,
-        name: 'CLAUDE.local.md',
-        scope: 'project',
-        load: 'always',
-        ...localInfo,
-        dir,
-        ...spreadImports(localInfo.path, localInfo.content),
-      });
     }
   }
 
@@ -260,7 +252,7 @@ function discoverMemorySources(projectPath) {
     for (const entry of entries) {
       if (!entry.isDirectory() || SKIP_DIRS.has(entry.name) || entry.name.startsWith('.')) continue;
       const subdir = path.join(dir, entry.name);
-      for (const name of ['CLAUDE.md', '.claude/CLAUDE.md']) {
+      for (const name of CLAUDE_MD_VARIANTS) {
         const filePath = path.join(subdir, name);
         if (seenPaths.has(filePath)) continue;
         const info = fileInfo(filePath);
@@ -268,8 +260,8 @@ function discoverMemorySources(projectPath) {
         seenPaths.add(filePath);
         const rel = path.relative(projectPath, subdir).replace(/\\/g, '/');
         sources.push({
-          id: `project-claude-md-${subdir.replace(/[^a-zA-Z0-9]/g, '-')}`,
-          name: `${rel}/${name.includes('/') ? '.claude/CLAUDE.md' : 'CLAUDE.md'}`,
+          id: `project-claude-md-${slug(name)}-${slug(subdir)}`,
+          name: `${rel}/${name}`,
           scope: 'project',
           load: 'tree',
           ...info,
@@ -293,7 +285,7 @@ function discoverMemorySources(projectPath) {
         id: `project-rule-${path.basename(file, '.md')}`,
         name: path.basename(file),
         scope: 'rule',
-        load: 'conditional',
+        load: hasPathsFilter(info.frontmatter) ? 'conditional' : 'always',
         ...info,
         ruleSource: 'project',
         ...spreadImports(info.path, info.content),
@@ -301,67 +293,61 @@ function discoverMemorySources(projectPath) {
     }
   }
 
-  // 6. Auto memory
-  const memoryDir = findMemoryDir(projectPath);
-  if (memoryDir && fs.existsSync(memoryDir)) {
-    const memoryMd = path.join(memoryDir, 'MEMORY.md');
+  function pushMemoryDir(dir, scope, idPrefix, extraFields = {}) {
+    const memoryMd = path.join(dir, 'MEMORY.md');
     const memInfo = fileInfo(memoryMd);
     if (memInfo) {
       sources.push({
-        id: 'memory-index',
+        id: `${idPrefix}-index`,
         name: 'MEMORY.md',
-        scope: 'memory',
+        scope,
         load: 'startup',
+        ...extraFields,
         ...memInfo,
         maxLines: 200,
         maxBytes: 25 * 1024,
         ...spreadImports(memInfo.path, memInfo.content),
       });
     }
-    for (const file of findMdFiles(memoryDir)) {
+    for (const file of findMdFiles(dir)) {
       if (path.basename(file) === 'MEMORY.md') continue;
       const info = fileInfo(file);
       if (!info) continue;
       sources.push({
-        id: `memory-${path.basename(file, '.md')}`,
+        id: `${idPrefix}-${path.basename(file, '.md')}`,
         name: path.basename(file),
-        scope: 'memory',
+        scope,
         load: 'ondemand',
+        ...extraFields,
         ...info,
         ...spreadImports(info.path, info.content),
       });
     }
   }
 
-  // 7. User-level memory (~/.claude/memory/)
-  const userMemoryDir = path.join(os.homedir(), '.claude', 'memory');
-  if (fs.existsSync(userMemoryDir)) {
-    const userMemoryMd = path.join(userMemoryDir, 'MEMORY.md');
-    const userMemInfo = fileInfo(userMemoryMd);
-    if (userMemInfo) {
-      sources.push({
-        id: 'user-memory-index',
-        name: 'MEMORY.md',
-        scope: 'user-memory',
-        load: 'startup',
-        ...userMemInfo,
-        maxLines: 200,
-        maxBytes: 25 * 1024,
-        ...spreadImports(userMemInfo.path, userMemInfo.content),
-      });
-    }
-    for (const file of findMdFiles(userMemoryDir)) {
-      if (path.basename(file) === 'MEMORY.md') continue;
-      const info = fileInfo(file);
-      if (!info) continue;
-      sources.push({
-        id: `user-memory-${path.basename(file, '.md')}`,
-        name: path.basename(file),
-        scope: 'user-memory',
-        load: 'ondemand',
-        ...info,
-        ...spreadImports(info.path, info.content),
-      });
+  // 6. Auto memory
+  const memoryDir = findMemoryDir(projectPath);
+  if (memoryDir && fs.existsSync(memoryDir)) {
+    pushMemoryDir(memoryDir, 'memory', 'memory');
+  }
+
+  // 7. Subagent persistent memory (https://code.claude.com/docs/en/sub-agents#enable-persistent-memory)
+  //    user:    ~/.claude/agent-memory/<agent>/
+  //    project: <project>/.claude/agent-memory/<agent>/
+  //    local:   <project>/.claude/agent-memory-local/<agent>/
+  const agentMemoryRoots = [
+    { root: path.join(os.homedir(), '.claude', 'agent-memory'), agentScope: 'user' },
+    { root: path.join(projectPath, '.claude', 'agent-memory'), agentScope: 'project' },
+    { root: path.join(projectPath, '.claude', 'agent-memory-local'), agentScope: 'local' },
+  ];
+  for (const { root, agentScope } of agentMemoryRoots) {
+    let agentDirs;
+    try { agentDirs = fs.readdirSync(root, { withFileTypes: true }); } catch { continue; }
+    for (const entry of agentDirs) {
+      if (!entry.isDirectory()) continue;
+      const agentName = entry.name;
+      const idPrefix = `agent-memory-${agentScope}-${agentName.replace(/[^a-zA-Z0-9]/g, '-')}`;
+      pushMemoryDir(path.join(root, agentName), 'agent-memory', idPrefix, { agentScope, agentName });
     }
   }
 
@@ -379,7 +365,7 @@ function discoverMemorySources(projectPath) {
     for (const { imp, parent, hard } of batch) {
       if (seen.has(imp)) {
         const existing = sourceByPath[imp];
-        if (existing && !existing.parentId && existing.scope === 'memory') {
+        if (existing && !existing.parentId && (existing.scope === 'memory' || existing.scope === 'agent-memory')) {
           existing.parentId = parent.id;
           if (hard) existing.load = 'import';
         }
@@ -553,13 +539,18 @@ app.post('/api/refresh', (_req, res) => {
   res.json({ ok: true });
 });
 
-app.delete('/api/file', (req, res) => {
-  const { path: filePath } = req.body || {};
-  if (!filePath) return res.status(400).json({ error: 'path required' });
+function resolveAllowedPath(filePath) {
+  if (!filePath) return { error: { status: 400, message: 'path required' } };
   const resolved = path.resolve(filePath.replace(/^~/, os.homedir()));
   const roots = [path.resolve(CLAUDE_DIR), path.resolve(currentProjectPath)];
   const inRoot = roots.some((r) => resolved === r || resolved.startsWith(r + path.sep));
-  if (!inRoot) return res.status(403).json({ error: 'path outside allowed roots' });
+  if (!inRoot) return { error: { status: 403, message: 'path outside allowed roots' } };
+  return { resolved };
+}
+
+app.delete('/api/file', (req, res) => {
+  const { resolved, error } = resolveAllowedPath(req.body?.path);
+  if (error) return res.status(error.status).json({ error: error.message });
   try {
     const stat = fs.statSync(resolved);
     if (!stat.isFile()) return res.status(400).json({ error: 'not a file' });
@@ -572,6 +563,37 @@ app.delete('/api/file', (req, res) => {
   }
 });
 
+app.post('/api/memory/cleanup-orphans', (req, res) => {
+  const { resolved, error } = resolveAllowedPath(req.body?.path);
+  if (error) return res.status(error.status).json({ error: error.message });
+  if (path.basename(resolved) !== 'MEMORY.md') return res.status(400).json({ error: 'not a MEMORY.md file' });
+  try {
+    const content = fs.readFileSync(resolved, 'utf-8');
+    const dir = path.dirname(resolved);
+    const lines = content.split('\n');
+    const removed = [];
+    const kept = [];
+    const linkRe = /^\s*-\s*\[([^\]]+)\]\(([^)]+\.md)\)/;
+    for (const line of lines) {
+      const m = line.match(linkRe);
+      if (m) {
+        const target = path.resolve(dir, m[2]);
+        if (!fs.existsSync(target)) {
+          removed.push({ name: m[1], file: m[2] });
+          continue;
+        }
+      }
+      kept.push(line);
+    }
+    if (removed.length === 0) return res.json({ ok: true, removed: [] });
+    fs.writeFileSync(resolved, kept.join('\n'), 'utf-8');
+    clearCache();
+    res.json({ ok: true, removed });
+  } catch (err) {
+    res.status(500).json({ error: err.message });
+  }
+});
+
 app.post('/api/open-in-editor', (req, res) => {
   const { path: filePath } = req.body;
   if (!filePath) return res.status(400).json({ error: 'path required' });