clay-server 4.1.0-beta.16 → 4.1.0-beta.18

package/lib/public/modules/sticky-notes-browser.js

@@ -4,9 +4,8 @@
 // the canvas over the conversation; this pane lists them, splits them into Open
 // and Closed, and is where a note is completed or brought back.
 //
-// Completion here is Close, never delete. A closed note leaves the active
-// canvas and moves to the Closed tab, where it stays readable and reversible.
-// There is deliberately no destructive control on this surface at all.
+// Completion here is Close. Permanent deletion is available only for closed
+// notes and always requires an explicit, accessible confirmation.
 
 import { store } from './store.js';
 import { iconHtml, refreshIcons } from './icons.js';
@@ -19,6 +18,10 @@ import { claimRightWorkbench, registerRightWorkbench, releaseRightWorkbench } fr
 var panel = null;
 var gridEl = null;
 var tabsEl = null;
+var deleteDialog = null;
+var deleteTrigger = null;
+var deleteRequestCounter = 0;
+var deleteRequestTimer = null;
 
 // Registered by app.js so this module never imports the other right-pane tools
 // and cannot form an import cycle with them.
@@ -63,11 +66,15 @@ function ensurePanel() {
       '</div>' +
     '</header>' +
     '<div id="notes-browser-tabs" class="notes-browser-tabs" role="tablist" aria-label="Sticky Notes state"></div>' +
-    '<div id="notes-browser-grid" class="notes-browser-grid" role="list"></div>';
+    '<div id="notes-browser-grid" class="notes-browser-grid" role="list"></div>' +
+    '<div id="notes-delete-dialog" class="notes-delete-dialog hidden" role="dialog" aria-modal="true" aria-labelledby="notes-delete-heading">' +
+      '<div class="notes-delete-dialog-card"><h2 id="notes-delete-heading">Delete this note permanently?</h2><p>This permanently removes the note. It cannot be restored.</p><p class="notes-delete-dialog-title"></p><p class="notes-delete-dialog-status" role="status"></p><div class="notes-delete-dialog-actions"><button type="button" data-action="cancel">Cancel</button><button type="button" class="danger" data-action="delete">Delete permanently</button></div></div>' +
+    '</div>';
   panels.appendChild(panel);
 
   gridEl = panel.querySelector("#notes-browser-grid");
   tabsEl = panel.querySelector("#notes-browser-tabs");
+  deleteDialog = panel.querySelector("#notes-delete-dialog");
 
   panel.querySelector("#notes-browser-close").addEventListener("click", closeNotesBrowser);
   panel.querySelector("#notes-browser-wide").addEventListener("click", function () {
@@ -76,6 +83,29 @@ function ensurePanel() {
   panel.querySelector("#notes-browser-fullscreen").addEventListener("click", function () {
     applyWindowState(store.get('notesBrowserWide'), !store.get('notesBrowserFullscreen'));
   });
+  deleteDialog.querySelector('[data-action="cancel"]').addEventListener("click", closeDeleteDialog);
+  deleteDialog.querySelector('[data-action="delete"]').addEventListener("click", confirmDelete);
+  deleteDialog.addEventListener("click", function (event) { if (event.target === deleteDialog) closeDeleteDialog(); });
+  deleteDialog.addEventListener("keydown", function (event) {
+    if (event.key === "Escape") {
+      event.preventDefault();
+      event.stopPropagation();
+      closeDeleteDialog(true);
+      return;
+    }
+    if (event.key !== "Tab") return;
+    var focusable = deleteDialog.querySelectorAll("button:not(:disabled), [href], input:not(:disabled), select:not(:disabled), textarea:not(:disabled), [tabindex]:not([tabindex='-1'])");
+    if (!focusable.length) return;
+    var first = focusable[0];
+    var last = focusable[focusable.length - 1];
+    if (event.shiftKey && document.activeElement === first) {
+      event.preventDefault();
+      last.focus();
+    } else if (!event.shiftKey && document.activeElement === last) {
+      event.preventDefault();
+      first.focus();
+    }
+  });
   refreshIcons();
 }
 
@@ -166,7 +196,8 @@ function buildCard(data) {
   title.textContent = getTitle(data.text) || "Untitled";
   header.appendChild(title);
 
-  // Exactly one lifecycle action per card, and it is never destructive.
+  // Closing and reopening are lifecycle actions; permanent deletion is offered
+  // separately below only because this card is known to be closed.
   var action = document.createElement("button");
   action.type = "button";
   action.className = "notes-browser-card-action";
@@ -200,6 +231,14 @@ function buildCard(data) {
   card.appendChild(body);
 
   if (closed) {
+    var deleteAction = document.createElement("button");
+    deleteAction.type = "button";
+    deleteAction.className = "notes-browser-card-action notes-browser-card-delete";
+    deleteAction.innerHTML = iconHtml("trash-2") + "<span>Delete permanently</span>";
+    deleteAction.title = "Permanently delete this closed note";
+    deleteAction.setAttribute("aria-label", "Delete permanently: " + title.textContent);
+    deleteAction.addEventListener("click", function (e) { e.stopPropagation(); openDeleteDialog(data, deleteAction); });
+    header.appendChild(deleteAction);
     var meta = document.createElement("p");
     meta.className = "notes-browser-card-meta";
     meta.textContent = closedMeta(data);
@@ -224,6 +263,77 @@ function buildCard(data) {
   return card;
 }
 
+function nextDeleteRequestId() {
+  deleteRequestCounter++;
+  return "delete-note-" + Date.now() + "-" + deleteRequestCounter;
+}
+
+function accountKey() {
+  return store.get('myUserId') ? String(store.get('myUserId')) : "single";
+}
+
+function openDeleteDialog(data, trigger) {
+  if (!deleteDialog || !data || !isClosed(data)) return;
+  deleteTrigger = trigger || null;
+  store.set({ notesDeletePending: { noteId: data.id, requestId: null, projectSlug: store.get('currentSlug') || null, accountKey: accountKey() } });
+  deleteDialog.querySelector(".notes-delete-dialog-title").textContent = getTitle(data.text) || "Untitled";
+  deleteDialog.querySelector(".notes-delete-dialog-status").textContent = "";
+  deleteDialog.querySelector('[data-action="delete"]').disabled = false;
+  deleteDialog.querySelector('[data-action="cancel"]').disabled = false;
+  deleteDialog.classList.remove("hidden");
+  deleteDialog.querySelector('[data-action="cancel"]').focus();
+}
+
+function closeDeleteDialog(force) {
+  var pending = store.get('notesDeletePending');
+  if (!force && pending && pending.requestId) return;
+  if (deleteRequestTimer) { clearTimeout(deleteRequestTimer); deleteRequestTimer = null; }
+  if (deleteDialog) deleteDialog.classList.add("hidden");
+  store.set({ notesDeletePending: null });
+  if (deleteTrigger && deleteTrigger.isConnected) deleteTrigger.focus();
+  deleteTrigger = null;
+}
+
+function confirmDelete() {
+  var pending = store.get('notesDeletePending');
+  if (!pending || !deleteDialog) return;
+  if (!store.get('connected')) {
+    deleteDialog.querySelector(".notes-delete-dialog-status").textContent = "Sticky Notes are unavailable while disconnected.";
+    return;
+  }
+  var requestId = nextDeleteRequestId();
+  store.set({ notesDeletePending: Object.assign({}, pending, { requestId: requestId }) });
+  deleteDialog.querySelector('[data-action="delete"]').disabled = true;
+  deleteDialog.querySelector('[data-action="cancel"]').disabled = true;
+  deleteDialog.querySelector(".notes-delete-dialog-status").textContent = "Deleting permanently...";
+  send({ type: "note_delete_permanently", id: pending.noteId, requestId: requestId });
+  deleteRequestTimer = setTimeout(function () {
+    var active = store.get('notesDeletePending');
+    if (!deleteDialog || !active || active.requestId !== requestId) return;
+    store.set({ notesDeletePending: Object.assign({}, active, { requestId: null }) });
+    deleteDialog.querySelector('[data-action="delete"]').disabled = false;
+    deleteDialog.querySelector('[data-action="cancel"]').disabled = false;
+    deleteDialog.querySelector(".notes-delete-dialog-status").textContent = "The delete request timed out. Try again.";
+    deleteRequestTimer = null;
+  }, 10000);
+}
+
+export function handleNoteDeleteResult(msg) {
+  var pending = store.get('notesDeletePending');
+  if (!deleteDialog || !msg || msg.projectSlug !== store.get('currentSlug') ||
+      msg.requestId !== (pending && pending.requestId) || !pending || msg.noteId !== pending.noteId ||
+      msg.projectSlug !== pending.projectSlug || pending.accountKey !== accountKey()) return;
+  if (deleteRequestTimer) { clearTimeout(deleteRequestTimer); deleteRequestTimer = null; }
+  if (msg.ok) {
+    closeDeleteDialog(true);
+    return;
+  }
+  store.set({ notesDeletePending: Object.assign({}, pending, { requestId: null }) });
+  deleteDialog.querySelector('[data-action="delete"]').disabled = false;
+  deleteDialog.querySelector('[data-action="cancel"]').disabled = false;
+  deleteDialog.querySelector(".notes-delete-dialog-status").textContent = msg.error || "The note could not be deleted.";
+}
+
 function emptyState(tab) {
   var empty = document.createElement("div");
   empty.className = "notes-browser-empty";
@@ -242,6 +352,11 @@ function emptyState(tab) {
 export function renderNotesBrowser() {
   if (!gridEl) return;
   var all = listNoteData();
+  var pending = store.get('notesDeletePending');
+  if (pending) {
+    var pendingCurrent = all.filter(function (item) { return item && item.id === pending.noteId; })[0];
+    if (!pendingCurrent || !isClosed(pendingCurrent)) closeDeleteDialog(true);
+  }
   var open = openNotes(all);
   var closed = closedNotes(all);
   renderTabs(open.length, closed.length);
@@ -284,6 +399,9 @@ export function openNotesBrowser() {
 }
 
 export function closeNotesBrowser() {
+  // Reset destructive UI state even when the panel was already closed. Right
+  // workbench/project transitions can race with panel visibility updates.
+  closeDeleteDialog(true);
   releaseRightWorkbench("notes-browser");
   if (!store.get('notesBrowserOpen')) return;
   if (panel) panel.classList.add("hidden");
@@ -304,10 +422,13 @@ export function initNotesBrowser() {
   registerRightWorkbench("notes-browser", closeNotesBrowser);
   document.addEventListener("keydown", function (e) {
     if (e.key !== "Escape") return;
+    if (deleteDialog && !deleteDialog.classList.contains("hidden")) return;
     if (!store.get('notesBrowserOpen')) return;
     closeNotesBrowser();
   });
   store.subscribe(function (state, previous) {
+    if (state.connected !== previous.connected || state.myUserId !== previous.myUserId ||
+        state.isMultiUserMode !== previous.isMultiUserMode) closeDeleteDialog(true);
     if (state.currentSlug === previous.currentSlug) return;
     // A different project starts from a closed, bounded, Open-tab pane.
     closeNotesBrowser();

package/lib/public/modules/sticky-notes.js

@@ -424,13 +424,12 @@ export function handleNoteWritten(msg) {
 // an older daemon on the other end of the socket still must not corrupt state.
 export function handleNoteDeleted(msg) {
   var entry = notes.get(msg.id);
-  if (!entry) return;
-  entry.el.remove();
+  if (entry) entry.el.remove();
+  clearNoteTimers(msg.id);
   notes.delete(msg.id);
   updateBadge();
   updateSidebarBadge();
 
-  clearNoteTimers(msg.id);
   refreshBrowser();
 }
 

package/lib/sdk-bridge.js

@@ -7,6 +7,7 @@ var usersModule = require("./users");
 var { getCodexConfig } = require("./codex-defaults");
 var { getKiroConfig } = require("./kiro-defaults");
 var { splitShellSegments, attachSkillDiscovery } = require("./sdk-skill-discovery");
+var skillDiscovery = require("./yoke/skill-discovery");
 var { isSafeBashSegment } = require("./safe-bash-commands");
 var { createMessageQueue } = require("./sdk-message-queue");
 var { attachMessageProcessor } = require("./sdk-message-processor");
@@ -162,6 +163,22 @@ function createSDKBridge(opts) {
     }];
   }
 
+  function getCodexSessionMcpServer(session, queryGeneration) {
+    if (!session || !Number.isInteger(queryGeneration)) return null;
+    var bridgeArgs = [
+      path.join(__dirname, "yoke", "mcp-bridge-server.js"),
+      "--port", String(clayPort),
+      "--slug", slug,
+      "--session", String(session.localId),
+      "--query-generation", String(queryGeneration),
+      "--session-only",
+    ];
+    if (clayTls) bridgeArgs.push("--tls");
+    var bridgeEnv = {};
+    if (clayAuthToken) bridgeEnv.CLAY_AUTH_TOKEN = clayAuthToken;
+    return { name: "clay-session-tools", command: process.execPath, args: bridgeArgs, env: bridgeEnv };
+  }
+
   function getFreshAuthState(force) {
     var now = Date.now();
     if (!force && _cachedFreshAuthState && now - _cachedFreshAuthAt < 15000) {
@@ -338,7 +355,7 @@ function createSDKBridge(opts) {
   }
 
   // --- Skill discovery (extracted to sdk-skill-discovery.js) ---
-  var skills = attachSkillDiscovery({ cwd: cwd });
+  var skills = attachSkillDiscovery({ cwd: cwd, getOptions: function () { return { env: getRuntimeEnv() }; } });
   var discoverSkillDirs = skills.discoverSkillDirs;
   var mergeSkills = skills.mergeSkills;
 
@@ -351,6 +368,19 @@ function createSDKBridge(opts) {
     return owner && owner.linuxUser ? owner.linuxUser : null;
   }
 
+  function getSessionSkillOptions(session) {
+    var runtimeEnv = getRuntimeEnv(session || {});
+    if (!osUsers) return { env: runtimeEnv };
+    var linuxUser = getSessionLinuxUser(session);
+    if (!linuxUser) return { disable: true };
+    try {
+      var info = require("./os-users").resolveOsUserInfo(linuxUser);
+      return Object.assign({}, skillDiscovery.optionsForOsUser(info), { env: runtimeEnv });
+    } catch (e) {
+      return { disable: true };
+    }
+  }
+
   var titleGenerator = sessionTitleGenerator.attachSessionTitleGenerator({
     sm: sm,
     cwd: cwd,
@@ -372,6 +402,7 @@ function createSDKBridge(opts) {
     adapter: adapter,
     saveImageFile: opts.saveImageFile,
     getSessionLinuxUser: getSessionLinuxUser,
+    getSessionSkillOptions: getSessionSkillOptions,
     onProcessingChanged: onProcessingChanged,
     onTurnDone: onTurnDone,
     onAutoTitle: function (session) { titleGenerator.generate(session); },
@@ -1004,7 +1035,8 @@ function createSDKBridge(opts) {
             && Number(session._sdkQueryGeneration || 0) === codexCatalogCandidate.generation
             && session.cliSessionId === msg.sessionId
             && (!sm.sessions || typeof sm.sessions.get !== "function" || sm.sessions.get(session.localId) === session)) {
-          session.codexDynamicToolCatalogVersion = codexCatalogCandidate.version;
+          if (codexCatalogCandidate.version) session.codexDynamicToolCatalogVersion = codexCatalogCandidate.version;
+          if (codexCatalogCandidate.issuesVersion) session.codexIssuesToolCatalogVersion = codexCatalogCandidate.issuesVersion;
           sm.saveSessionFile(session);
           codexCatalogCandidate = null;
         }
@@ -1574,7 +1606,11 @@ function createSDKBridge(opts) {
     if (linuxUser) {
       claudeOpts.linuxUser = linuxUser;
       claudeOpts.singleTurn = !!session.singleTurn;
-      claudeOpts.originalHome = require("./config").REAL_HOME || null;
+      try {
+        claudeOpts.originalHome = require("./os-users").resolveOsUserInfo(linuxUser).home;
+      } catch (e) {
+        claudeOpts.originalHome = null;
+      }
       claudeOpts.projectPath = session.cwd || null;
       claudeOpts._perfT0 = t0;
       // Pass previous worker state for reuse
@@ -1616,6 +1652,17 @@ function createSDKBridge(opts) {
     // delivered by this provider.
     var sessionToolDefs = getSessionToolDefs(session) || [];
     var queryGeneration = Number(session._sdkQueryGeneration || 0);
+    var hasIssueCatalog = false;
+    for (var issueToolIndex = 0; issueToolIndex < sessionToolDefs.length; issueToolIndex++) {
+      if (sessionToolDefs[issueToolIndex].name === "create_issue") {
+        hasIssueCatalog = true;
+        break;
+      }
+    }
+    var recoverCodexIssueTools = sessionAdapter.vendor === "codex"
+      && !!session.cliSessionId
+      && hasIssueCatalog
+      && Number(session.codexIssuesToolCatalogVersion || 0) < 1;
     function queryContextAvailable() {
       if (Number(session._sdkQueryGeneration || 0) !== queryGeneration) return false;
       if (sm && sm.sessions && typeof sm.sessions.get === "function" && sm.sessions.get(session.localId) !== session) return false;
@@ -1750,6 +1797,7 @@ function createSDKBridge(opts) {
       cwd: cwd,
       linuxUser: linuxUser || undefined,
       env: sessionRuntimeEnv,
+      skillOptions: getSessionSkillOptions(session),
       // appendSystemPrompt, NOT systemPrompt: a plain-string systemPrompt
       // REPLACES the entire Claude Code system prompt (sdk.d.ts:2096), which
       // would strip the driver session down to the two-sentence pair preset.
@@ -1771,6 +1819,9 @@ function createSDKBridge(opts) {
       toolServers: mergedMcpServers,
       toolServerDescriptors: extractMcpDescriptors(mergedMcpServers) || undefined,
       dynamicTools: sessionToolDefs,
+      // Codex persists dynamic tools with a thread. A stale authorized Driver
+      // gets this exact-query bridge; its handlers still reauthorize live.
+      sessionMcpServer: recoverCodexIssueTools ? getCodexSessionMcpServer(session, queryGeneration) : undefined,
       callDynamicTool: function (toolName, args) {
         var toolDef = findSessionToolDef(toolName);
         if (toolDef && typeof toolDef.handler === "function") {
@@ -1957,6 +2008,12 @@ function createSDKBridge(opts) {
       if (completeInterviewCatalog || requiredCatalogTools.report_scheduled_task_outcome) {
         codexCatalogCandidate = { generation: queryGeneration, version: yoke.sessionTools.CODEX_CATALOG_VERSION };
       }
+      if (hasIssueCatalog) {
+        codexCatalogCandidate = Object.assign({}, codexCatalogCandidate || {}, {
+          generation: queryGeneration,
+          issuesVersion: 1,
+        });
+      }
     }
     session.streamPromise = processQueryStream(session, codexCatalogCandidate).catch(function(err) {
     });
@@ -2199,22 +2256,9 @@ function createSDKBridge(opts) {
           slug: slug,
         });
 
-        var fsSkills = discoverSkillDirs();
-        sm.skillNames = mergeSkills(result.skills, fsSkills);
-        if (result.slashCommands) {
-          var seen = new Set();
-          var combined = [];
-          var all = result.slashCommands.concat(Array.from(sm.skillNames));
-          for (var k = 0; k < all.length; k++) {
-            if (!seen.has(all[k])) {
-              seen.add(all[k]);
-              combined.push(all[k]);
-            }
-          }
-          sm.slashCommands = combined;
-          sm.setSlashCommandsForVendor(defaultVendor, combined);
-          send({ type: "slash_commands", commands: combined, vendor: defaultVendor });
-        }
+        // Skill and slash-command catalogs are session-owned. The warmup has
+        // no authenticated session target, so never publish its personal
+        // inventory through the project-wide session manager or broadcast.
         if (result.defaultModel) {
           sm.defaultModelByVendor = sm.defaultModelByVendor || {};
           sm.defaultModelByVendor[defaultVendor] = sm.defaultModelByVendor[defaultVendor] || result.defaultModel;

package/lib/sdk-message-processor.js

@@ -28,6 +28,7 @@ function attachMessageProcessor(ctx) {
   var mergeSkills = ctx.mergeSkills;
   var saveImageFile = ctx.saveImageFile;
   var getSessionLinuxUser = ctx.getSessionLinuxUser || function () { return null; };
+  var getSessionSkillOptions = ctx.getSessionSkillOptions || function () { return {}; };
 
   function getMateIdForNotification() {
     if (!isMate) return null;
@@ -208,21 +209,26 @@ function attachMessageProcessor(ctx) {
       session.activeBackgroundTasks = [];
       sendToSession(session, { type: "active_background_tasks", tasks: [] });
       if (previousBackgroundTaskCount !== 0) sm.broadcastSessionList();
-      var fsSkills = discoverSkillDirs();
-      sm.skillNames = mergeSkills(parsed.skills, fsSkills);
+      var fsSkills = discoverSkillDirs(getSessionSkillOptions(session));
+      session.skillNames = Array.from(mergeSkills(parsed.skills, fsSkills));
       if (parsed.slashCommands) {
         // Union: SDK slash_commands + merged skills (deduplicated)
+        session.vendorSlashCommands = parsed.slashCommands.filter(function (name) {
+          return session.skillNames.indexOf(name) === -1;
+        });
         var seen = new Set();
         var combined = [];
-        var all = parsed.slashCommands.concat(Array.from(sm.skillNames));
+        var all = session.vendorSlashCommands.concat(session.skillNames);
         for (var k = 0; k < all.length; k++) {
           if (!seen.has(all[k])) {
             seen.add(all[k]);
             combined.push(all[k]);
           }
         }
-        sm.slashCommands = combined;
-        send({ type: "slash_commands", commands: sm.slashCommands });
+        session.slashCommands = combined;
+        session.slashCommandsByVendor = session.slashCommandsByVendor || {};
+        session.slashCommandsByVendor[session.vendor || (adapter && adapter.vendor) || "claude"] = combined;
+        sendToSession(session, { type: "slash_commands", commands: combined, vendor: session.vendor || (adapter && adapter.vendor) || "claude" });
       }
       if (parsed.model) {
         var initVendor = session.vendor || (adapter && adapter.vendor) || "claude";
@@ -899,15 +905,20 @@ function attachMessageProcessor(ctx) {
       // init) and push a full replacement to the client.
       var cmdSeen = new Set();
       var cmdCombined = [];
-      var cmdAll = (parsed.commandNames || []).concat(Array.from(sm.skillNames || []));
+      session.vendorSlashCommands = (parsed.commandNames || []).filter(function (name) {
+        return (session.skillNames || []).indexOf(name) === -1;
+      });
+      var cmdAll = session.vendorSlashCommands.concat(session.skillNames || []);
       for (var ci = 0; ci < cmdAll.length; ci++) {
         if (!cmdSeen.has(cmdAll[ci])) {
           cmdSeen.add(cmdAll[ci]);
           cmdCombined.push(cmdAll[ci]);
         }
       }
-      sm.slashCommands = cmdCombined;
-      send({ type: "slash_commands", commands: sm.slashCommands });
+      session.slashCommands = cmdCombined;
+      session.slashCommandsByVendor = session.slashCommandsByVendor || {};
+      session.slashCommandsByVendor[session.vendor || (adapter && adapter.vendor) || "claude"] = cmdCombined;
+      sendToSession(session, { type: "slash_commands", commands: cmdCombined, vendor: session.vendor || (adapter && adapter.vendor) || "claude" });
 
     } else if (parsed.yokeType === "worker_shutting_down") {
       // Surface non-routine teardown reasons; "host_exit" is the normal close.

package/lib/sdk-skill-discovery.js

@@ -1,5 +1,4 @@
-var fs = require("fs");
-var path = require("path");
+var skillDiscovery = require("./yoke/skill-discovery");
 
 // Split shell command on operators (&&, ||, ;, |) while respecting quotes
 // and parentheses. Returns array of command segments.
@@ -79,34 +78,13 @@ function splitShellSegments(cmd) {
 
 function attachSkillDiscovery(ctx) {
   var cwd = ctx.cwd;
+  var getOptions = ctx.getOptions || function () { return {}; };
 
-  function discoverSkillDirs() {
+  function discoverSkillDirs(options) {
+    var discovered = skillDiscovery.discoverSkills(cwd, options || getOptions());
     var skills = {};
-    var dirs = [
-      path.join(require("./config").REAL_HOME, ".claude", "skills"),
-      path.join(cwd, ".claude", "skills"),
-    ];
-    for (var d = 0; d < dirs.length; d++) {
-      var base = dirs[d];
-      var entries;
-      try {
-        entries = fs.readdirSync(base, { withFileTypes: true });
-      } catch (e) {
-        continue; // directory doesn't exist
-      }
-      for (var i = 0; i < entries.length; i++) {
-        var entry = entries[i];
-        if (!entry.isDirectory() && !entry.isSymbolicLink()) continue;
-        var skillDir = path.join(base, entry.name);
-        var skillMd = path.join(skillDir, "SKILL.md");
-        try {
-          fs.accessSync(skillMd, fs.constants.R_OK);
-          // project skills override global skills with same name
-          skills[entry.name] = skillDir;
-        } catch (e) {
-          // no SKILL.md, skip
-        }
-      }
+    for (var i = 0; i < discovered.length; i++) {
+      skills[discovered[i].name] = discovered[i].path.replace(/\/SKILL\.md$/, "");
     }
     return skills;
   }

package/lib/sessions.js

@@ -24,6 +24,7 @@ function createSessionManager(opts) {
   var sessionViewedListeners = [];
   var onSessionRenamed = opts.onSessionRenamed || function () {};
   var onSessionIdentityAssigned = opts.onSessionIdentityAssigned || function () {};
+  var onSessionHydrate = opts.onSessionHydrate || null;
 
   // --- Multi-session state ---
   var nextLocalId = 1;
@@ -162,6 +163,7 @@ function createSessionManager(opts) {
       if (session.ownerId) metaObj.ownerId = session.ownerId;
       if (session.vendor) metaObj.vendor = session.vendor;
       if (session.codexDynamicToolCatalogVersion) metaObj.codexDynamicToolCatalogVersion = session.codexDynamicToolCatalogVersion;
+      if (session.codexIssuesToolCatalogVersion) metaObj.codexIssuesToolCatalogVersion = session.codexIssuesToolCatalogVersion;
       if (session.model) metaObj.model = session.model;
       if (session.effort) metaObj.effort = session.effort;
       // Persist the session's "born" mode so TUI sessions reappear after a
@@ -317,6 +319,7 @@ function createSessionManager(opts) {
       };
       if (m.vendor) session.vendor = m.vendor;
       session.codexDynamicToolCatalogVersion = Number(m.codexDynamicToolCatalogVersion || 0);
+      session.codexIssuesToolCatalogVersion = Number(m.codexIssuesToolCatalogVersion || 0);
       session.model = m.model || deriveSessionModel(loaded[i].history);
       session.effort = m.effort || null;
       if (m.loop) session.loop = m.loop;
@@ -797,6 +800,7 @@ function createSessionManager(opts) {
   function switchSession(localId, targetWs, transform) {
     var session = sessions.get(localId);
     if (!session) return;
+    if (typeof onSessionHydrate === "function") onSessionHydrate(session);
 
     // Pane sockets (split-view iframes) pin their session via switch_session
     // but must not move the project-global active pointer: reloads and
@@ -824,7 +828,9 @@ function createSessionManager(opts) {
     var _vendorCaps = _capsByVendor[_sessionVendor] || {};
     _send({ type: "session_switched", id: localId, cliSessionId: session.cliSessionId || null, loop: session.loop || null, vendor: session.vendor || null, model: session.model || null, effort: session.effort || null, hasHistory: (session.history && session.history.length > 0), capabilities: _vendorCaps, isProcessing: !!session.isProcessing, mode: session.mode || "gui", terminalId: typeof session.terminalId === "number" ? session.terminalId : null, runtimeMode: session.runtimeMode || null, runtimeTerminalId: typeof session.runtimeTerminalId === "number" ? session.runtimeTerminalId : null, tuiSuspended: !!session.tuiSuspended, dangerouslySkipPermissions: !!session.dangerouslySkipPermissions, permissionMode: session.permissionMode || null, autonomousRun: projectAutonomousRun(session.autonomousRun), loopInterviewBrief: session.loopInterviewBrief || null, loopInterviewHandoff: session.loopInterviewHandoff || null, scheduledTaskDraft: session.scheduledTaskDraft || null });
     // Send vendor-specific slash commands
-    var _vendorCmds = slashCommandsByVendor[_sessionVendor] || slashCommands || [];
+    var _vendorCmds = (session.slashCommandsByVendor && session.slashCommandsByVendor[_sessionVendor])
+      || session.slashCommands
+      || [];
     _send({ type: "slash_commands", commands: _vendorCmds, vendor: _sessionVendor });
     broadcastSessionList();
     replayHistory(session, undefined, targetWs, transform);
@@ -1288,6 +1294,7 @@ function createSessionManager(opts) {
   }
 
   return {
+    setSessionHydrator: function (fn) { onSessionHydrate = typeof fn === "function" ? fn : null; },
     get activeSessionId() { return activeSessionId; },
     get nextLocalId() { return nextLocalId; },
     get slashCommands() { return slashCommands; },

package/lib/yoke/adapters/acp.js

@@ -44,6 +44,7 @@ function createAcpAdapter(vendor, opts) {
   var defaultModel = driver.defaultModel || cachedModels[0] || "auto";
   var activeHandles = [];
   var lastActiveAt = Date.now();
+  var skillEnv = opts.env || process.env;
 
   function context(extra) {
     return Object.assign({
@@ -96,7 +97,7 @@ function createAcpAdapter(vendor, opts) {
   }
 
   function readyResult() {
-    var skills = skillDiscovery.discoverSkills(cwd).map(function(skill) { return skill.name; });
+    var skills = skillDiscovery.discoverSkills(cwd, { env: skillEnv }).map(function(skill) { return skill.name; });
     var result = {
       models: cachedModels.slice(),
       defaultModel: defaultModel,
@@ -220,7 +221,7 @@ function createAcpAdapter(vendor, opts) {
       if (!initialized || !acp || !acp.started) await adapter.init(queryOpts);
       if (shuttingDown) throw new Error(driver.displayName + " adapter is shutting down");
       var controller = queryOpts.abortController || new AbortController();
-      var sharedSkills = queryOpts.skipSkills ? [] : skillDiscovery.discoverSkills(queryOpts.cwd || cwd);
+      var sharedSkills = queryOpts.skipSkills ? [] : skillDiscovery.discoverSkills(queryOpts.cwd || cwd, queryOpts.skillOptions || { env: queryOpts.env || skillEnv });
       var skillIndex = skillDiscovery.buildSkillIndex(sharedSkills);
       var acpOptions = (queryOpts.adapterOptions && queryOpts.adapterOptions.ACP) || {};
       var handle = null;

package/lib/yoke/adapters/antigravity.js

@@ -353,12 +353,12 @@ function createAntigravityAdapter(opts) {
 
   var adapter = {
     vendor: "antigravity",
-    init: async function() {
+    init: async function(initOpts) {
       if (!binaryPath) binaryPath = findBinary();
       if (!binaryPath) throw new Error("Antigravity CLI binary not found: agy");
       var fetched = opts._fetchModels ? await opts._fetchModels(binaryPath, cwd) : await fetchModels(binaryPath, cwd);
       if (fetched && fetched.length) cachedModels = fetched;
-      var skills = skillDiscovery.discoverSkills(cwd).map(function(skill) { return skill.name; });
+      var skills = skillDiscovery.discoverSkills(cwd, { env: (initOpts && initOpts.env) || null }).map(function(skill) { return skill.name; });
       return {
         models: cachedModels.slice(),
         defaultModel: cachedModels[0] || "auto",