clay-server 4.2.0-beta.1 → 4.2.0-beta.2

package/lib/public/index.html

@@ -408,9 +408,14 @@
           <span class="header-title" id="header-title">Connecting...</span>
           <button id="header-rename-btn" type="button" title="Rename session"><i data-lucide="pencil"></i></button>
           <button id="header-info-btn" type="button" title="Session info"><i data-lucide="info"></i></button>
-          <button id="header-full-access-btn" type="button" class="session-full-access hidden" role="switch" aria-checked="false" title="Skip Permissions is off — permission prompts are on">
-            <span class="session-full-access-label">Skip Permissions</span><span class="session-full-access-track" aria-hidden="true"><span></span></span>
-          </button>
+          <div id="header-full-access-btn" class="session-permission-control hidden" role="group" aria-label="Session permission mode">
+            <div class="session-permission-segmented">
+              <button type="button" data-permission-mode="default">Ask</button>
+              <button type="button" data-permission-mode="auto">Auto</button>
+              <button type="button" data-permission-mode="bypassPermissions" aria-label="Skip permissions"><span class="permission-label-long">Skip permissions</span><span class="permission-label-short" aria-hidden="true">Skip</span></button>
+            </div>
+            <span class="session-permission-status hidden" aria-live="polite"></span>
+          </div>
           <button type="button" id="header-tui-close-btn" class="header-tui-close-btn hidden" title="Close terminal (keeps history, resume anytime)" aria-label="Close terminal"><i data-lucide="power"></i></button>
           <div id="mate-mobile-title" class="mate-mobile-title hidden">
             <img id="mate-mobile-avatar" class="mate-mobile-avatar" alt="">

package/lib/public/modules/app-connection.js

@@ -20,6 +20,8 @@ import { beginDefaultAiConnection, requestDefaultAi } from './default-ai.js';
 import { beginContextViewConnection, requestContextView } from './context-view-preference.js';
 import { beginDefaultVendorConnection, requestDefaultVendor } from './default-vendor.js';
 import { clearProjectSplitState } from './split-session-boundary.js';
+import { clearPermissionModePending } from './permission-control.js';
+import { clearMcpPermissionModePending } from './mcp-ui.js';
 
 var reconnectTimer = null;
 var reconnectDelay = 1000;
@@ -165,6 +167,8 @@ export function setStatus(status) {
   } else if (status === "processing") {
     store.set({ processing: true });
   } else {
+    clearPermissionModePending();
+    clearMcpPermissionModePending();
     store.set({ connected: false, processing: false });
   }
 }

package/lib/public/modules/app-header.js

@@ -12,7 +12,7 @@ import { saveToolState, resetToolState, restoreToolState } from './tools.js';
 import { getSessionUsage, setSessionUsage, getContextData, setContextData, updateContextPanel, updateUsagePanel } from './app-panels.js';
 import { onHistoryPrepended as onSessionSearchHistoryPrepended } from './session-search.js';
 import { getCachedSessions } from './sidebar-sessions.js';
-import { showConfirm } from './app-misc.js';
+import { bindPermissionControl, renderPermissionControl } from './permission-control.js';
 
 // --- Module-owned state ---
 var sessionInfoPopover = null;
@@ -24,37 +24,30 @@ export function initHeader() {
   var headerInfoBtn = document.getElementById("header-info-btn");
   var headerFullAccessBtn = document.getElementById("header-full-access-btn");
 
-  function updateFullAccessButton() {
-    if (!headerFullAccessBtn) return;
+  function permissionControlState() {
     var s = store.snap();
-    var visible = !s.dmMode && !s.splitPanes && !s.skipPermsEnabled && s.activeSessionMode === "gui" && !!s.activeSessionId;
-    var enabled = !!s.sessionFullAccess;
-    headerFullAccessBtn.classList.toggle("hidden", !visible);
-    headerFullAccessBtn.classList.toggle("active", enabled);
-    headerFullAccessBtn.setAttribute("aria-checked", enabled ? "true" : "false");
-    headerFullAccessBtn.title = enabled ? "Skip Permissions is on — click to restore permission prompts" : "Skip Permissions is off — permission prompts are on";
+    return {
+      projectSlug: s.currentSlug,
+      sessionId: s.activeSessionId,
+      vendor: s.currentVendor || "claude",
+      permissionMode: s.currentMode,
+      effectivePermissionMode: s.effectivePermissionMode,
+      permissionCapabilities: s.permissionCapabilities,
+      connected: s.connected,
+      globalPermissionModeForced: s.skipPermsEnabled === true,
+      visible: !s.dmMode && !s.splitPanes && s.activeSessionMode === "gui" && !!s.activeSessionId,
+    };
   }
 
-  function sendFullAccess(enabled) {
-    var ws = getWs();
-    var id = store.get('activeSessionId');
-    if (ws && ws.readyState === 1 && id) {
-      ws.send(JSON.stringify({ type: "set_session_full_access", id: id, enabled: enabled }));
-    }
+  function updateFullAccessButton() {
+    if (!headerFullAccessBtn) return;
+    renderPermissionControl(headerFullAccessBtn, permissionControlState());
   }
 
   if (headerFullAccessBtn) {
-    headerFullAccessBtn.addEventListener("click", function () {
-      if (store.get('sessionFullAccess')) {
-        sendFullAccess(false);
-        return;
-      }
-      showConfirm("Skip permission prompts for this session? Tool requests will be approved automatically.", function () {
-        sendFullAccess(true);
-      }, "Skip Permissions", true);
-    });
+    bindPermissionControl(headerFullAccessBtn, permissionControlState);
     store.subscribe(function (state, prev) {
-      if (state.sessionFullAccess !== prev.sessionFullAccess || state.activeSessionId !== prev.activeSessionId ||
+      if (state.currentMode !== prev.currentMode || state.effectivePermissionMode !== prev.effectivePermissionMode || state.permissionCapabilities !== prev.permissionCapabilities || state.permissionModePendingByTarget !== prev.permissionModePendingByTarget || state.connected !== prev.connected || state.activeSessionId !== prev.activeSessionId || state.currentSlug !== prev.currentSlug || state.currentVendor !== prev.currentVendor ||
           state.activeSessionMode !== prev.activeSessionMode ||
           state.dmMode !== prev.dmMode || state.splitPanes !== prev.splitPanes ||
           state.skipPermsEnabled !== prev.skipPermsEnabled) updateFullAccessButton();

package/lib/public/modules/app-messages.js

@@ -54,7 +54,8 @@ import { showRewindModal, onRewindComplete, setRewindMode, onRewindError, clearP
 import { checkAdminAccess } from './admin.js';
 import { mateAvatarUrl } from './avatar.js';
 import { showImageModal, sendExtensionCommand, handleMcpToolCallMessage } from './app-misc.js';
-import { handleMcpServersState } from './mcp-ui.js';
+import { handleMcpServersState, handleMcpPermissionModeResult } from './mcp-ui.js';
+import { handlePermissionModeResult } from './permission-control.js';
 import { handleShellCommandResult } from './shell-command.js';
 import { handleLoopRegistryUpdated, handleScheduleRunStarted, handleScheduleRunFinished, handleLoopScheduled, isSchedulerOpen, enterCraftingMode, exitCraftingMode, handleLoopRegistryFiles } from './scheduler.js';
 import { handleScheduledTaskMessage, handleScheduledTaskSessionSwitched } from './scheduled-tasks.js';
@@ -374,11 +375,9 @@ export function processMessage(msg) {
         if (msg.ownerLocked !== undefined) store.set({ ownerLocked: !!msg.ownerLocked });
         if (msg.osUsers !== undefined) store.set({ isOsUsers: !!msg.osUsers });
         if (msg.lanHost) window.__lanHost = msg.lanHost;
-        if (msg.dangerouslySkipPermissions) {
-          store.set({ skipPermsEnabled: true });
-          var spBanner = document.getElementById("skip-perms-pill");
-          if (spBanner) spBanner.classList.remove("hidden");
-        }
+        store.set({ skipPermsEnabled: msg.dangerouslySkipPermissions === true });
+        var spBanner = document.getElementById("skip-perms-pill");
+        if (spBanner) spBanner.classList.toggle("hidden", msg.dangerouslySkipPermissions !== true);
         updateProjectList(msg);
         refreshProjectSessionVisibilitySettings(msg.projects);
         break;
@@ -555,6 +554,9 @@ export function processMessage(msg) {
           }
         }
         if (msg.mode) _cs.currentMode = msg.mode;
+        if (Object.prototype.hasOwnProperty.call(msg, 'effectivePermissionMode')) _cs.effectivePermissionMode = msg.effectivePermissionMode;
+        if (msg.permissionCapabilities) _cs.permissionCapabilities = msg.permissionCapabilities;
+        if (msg.mcpPermissionModeOverrides) _cs.mcpPermissionModeOverrides = msg.mcpPermissionModeOverrides;
         if (msg.effort) _cs.currentEffort = msg.effort;
         if (msg.betas) _cs.currentBetas = msg.betas;
         if (msg.thinking) _cs.currentThinking = msg.thinking;
@@ -823,7 +825,7 @@ export function processMessage(msg) {
         var _effectiveTerminalId = (typeof msg.runtimeTerminalId === "number")
           ? msg.runtimeTerminalId
           : (typeof msg.terminalId === "number" ? msg.terminalId : null);
-        store.set({ activeSessionId: msg.id, cliSessionId: msg.cliSessionId || null, currentModel: msg.model || "", currentEffort: msg.effort || store.get('currentEffort'), vendorCapabilities: msg.capabilities || {}, sessionIsProcessing: !!msg.isProcessing, activeSessionMode: _effectiveMode, activeTerminalId: _effectiveTerminalId, sessionHasHistory: !!msg.hasHistory, sessionVendorBound: !!msg.vendor || !!msg.hasHistory, sessionFullAccess: msg.permissionMode === "bypassPermissions", currentMode: msg.permissionMode || store.get('currentMode') });
+        store.set({ activeSessionId: msg.id, cliSessionId: msg.cliSessionId || null, currentModel: msg.model || "", currentEffort: msg.effort || store.get('currentEffort'), vendorCapabilities: msg.capabilities || {}, sessionIsProcessing: !!msg.isProcessing, activeSessionMode: _effectiveMode, activeTerminalId: _effectiveTerminalId, sessionHasHistory: !!msg.hasHistory, sessionVendorBound: !!msg.vendor || !!msg.hasHistory, sessionFullAccess: msg.permissionMode === "bypassPermissions", currentMode: msg.permissionMode || store.get('currentMode'), effectivePermissionMode: msg.effectivePermissionMode || null, permissionCapabilities: msg.permissionCapabilities || { auto: false, mcpOverride: false }, mcpPermissionModeOverrides: msg.mcpPermissionModeOverrides || {} });
         handleScheduledTaskSessionSwitched(msg);
         requestLoopInterviewState();
         replayPendingMessages(msg.id);
@@ -1598,6 +1600,14 @@ export function processMessage(msg) {
         handleMcpServersState(msg);
         break;
 
+      case "mcp_permission_mode_result":
+        handleMcpPermissionModeResult(msg);
+        break;
+
+      case "permission_mode_result":
+        handlePermissionModeResult(msg);
+        break;
+
       case "term_created":
         // Login terminals never come through here: they are created by the
         // server-owned flow and announced with vendor_login_ready instead.

package/lib/public/modules/app-panels.js

@@ -8,6 +8,7 @@ import { getWs } from './ws-ref.js';
 import { getContextView as getStoredContextView, getEffectiveContextView, setContextView as setStoredContextView } from './context-view-preference.js';
 import { reportPaneContext } from './pane-bridge.js';
 import { setupModelPicker, renderModelPicker, requestVendorModels, prepareModelPickerOpen, modelDisplayName } from './model-picker.js';
+import { sendPermissionMode } from './permission-control.js';
 
 // --- Module-owned state (not in store) ---
 var sessionUsage = { cost: 0, input: 0, output: 0, cacheRead: 0, cacheWrite: 0, turns: 0 };
@@ -85,11 +86,12 @@ var contextMiniLabel = null;
 
 // --- Constants ---
 var MODE_OPTIONS = [
-  { value: "default", label: "Default" },
+  { value: "default", label: "Ask" },
   { value: "plan", label: "Plan" },
   { value: "acceptEdits", label: "Auto-accept edits" },
 ];
-var MODE_FULL_AUTO = { value: "bypassPermissions", label: "Full auto" };
+var MODE_FULL_AUTO = { value: "auto", label: "Auto" };
+var MODE_SKIP = { value: "bypassPermissions", label: "Skip permissions" };
 var EFFORT_LEVELS = ["low", "medium", "high", "xhigh", "max"];
 var EFFORT_LEVELS_BY_VENDOR = {
   claude: ["low", "medium", "high", "xhigh", "max"],
@@ -142,7 +144,8 @@ function modeDisplayName(value) {
   for (var i = 0; i < MODE_OPTIONS.length; i++) {
     if (MODE_OPTIONS[i].value === value) return MODE_OPTIONS[i].label;
   }
-  if (value === "bypassPermissions") return "Full auto";
+  if (value === "auto") return "Auto";
+  if (value === "bypassPermissions") return "Skip permissions";
   if (value === "dontAsk") return "Don\u2019t ask";
   return value;
 }
@@ -196,22 +199,29 @@ function rebuildModeList() {
   if (!configModeList) return;
   configModeList.innerHTML = "";
   var options = MODE_OPTIONS.slice();
-  if (store.get('skipPermsEnabled')) {
-    options.push(MODE_FULL_AUTO);
-  }
+  options.push(MODE_FULL_AUTO);
+  options.push(MODE_SKIP);
+  var autoSupported = store.get('permissionCapabilities').auto === true;
+  var globallyForced = store.get('skipPermsEnabled') === true;
   for (var i = 0; i < options.length; i++) {
     var opt = options[i];
     var btn = document.createElement("button");
     btn.className = "config-radio-item";
-    if (opt.value === store.get('currentMode')) btn.classList.add("active");
+    if (opt.value === (globallyForced ? "bypassPermissions" : store.get('currentMode'))) btn.classList.add("active");
     btn.dataset.mode = opt.value;
     btn.textContent = opt.label;
+    if (opt.value === "auto" && !autoSupported) {
+      btn.disabled = true;
+      btn.title = "Auto permissions require a Claude session.";
+      btn.setAttribute("aria-description", "Unavailable because this is not a Claude session.");
+    }
+    if (globallyForced) {
+      btn.disabled = true;
+      btn.title = "Skip permissions is forced by the server setting.";
+    }
     btn.addEventListener("click", function () {
       var mode = this.dataset.mode;
-      var ws = getWs();
-      if (ws && ws.readyState === 1) {
-        ws.send(JSON.stringify({ type: "set_permission_mode", mode: mode }));
-      }
+      sendPermissionMode(store.get('currentSlug'), store.get('activeSessionId'), mode);
       configPopover.classList.add("hidden");
       configChip.classList.remove("active");
     });
@@ -420,6 +430,7 @@ export function initPanels() {
         state.codexApproval !== prev.codexApproval ||
         state.codexSandbox !== prev.codexSandbox ||
         state.codexWebSearch !== prev.codexWebSearch ||
+        state.skipPermsEnabled !== prev.skipPermsEnabled ||
         state.sessionHasHistory !== prev.sessionHasHistory ||
         state.activeSessionMode !== prev.activeSessionMode) {
       updateConfigChip();

package/lib/public/modules/clay-file-links.js

@@ -3,6 +3,7 @@
 import { escapeHtml } from './utils.js';
 import { refreshIcons } from './icons.js';
 import { store } from './store.js';
+import { forwardPaneFileReference } from './pane-bridge.js';
 
 var openFileHandler = null;
 var delegatedBinding = false;
@@ -99,6 +100,12 @@ function bindDelegatedHandler() {
   document.addEventListener("click", function (event) {
     var button = event.target && event.target.closest ? event.target.closest(".clay-file-link") : null;
     if (!button) return;
+    if (store.get('paneMode') && forwardPaneFileReference(button.dataset.filePath, {
+      line: button.dataset.fileLine ? Number(button.dataset.fileLine) : null,
+      column: button.dataset.fileColumn ? Number(button.dataset.fileColumn) : null,
+      projectSlug: button.dataset.fileProjectSlug || null,
+      sessionId: button.dataset.fileSessionId || null
+    })) return;
     if (!openFileHandler) { showUnavailable(button); return; }
     var result = openFileHandler(button.dataset.filePath, {
       line: button.dataset.fileLine ? Number(button.dataset.fileLine) : null,

package/lib/public/modules/clay-log-links.js

@@ -1,4 +1,5 @@
 import { enhanceClayIssueLinks, isExactClayIssueReference } from './clay-issue-links.js';
+import { enhanceGithubLinks } from './github-links.js';
 
 export function renderClayRecordLink(href, text) {
   if (!isExactClayLogReference(href) && !isExactClayIssueReference(href)) return null;
@@ -80,4 +81,7 @@ export function enhanceClayLogLinks(root) {
     fragment.appendChild(document.createTextNode(text.slice(offset)));
     nodes[i].parentNode.replaceChild(fragment, nodes[i]);
   }
+  // Issues and Logs call this enhancer directly, without the transcript
+  // session-link pass. Keep external GitHub chips common to those surfaces.
+  enhanceGithubLinks(root);
 }

package/lib/public/modules/github-links.js

@@ -0,0 +1,115 @@
+import { escapeHtml } from './utils.js';
+import { iconHtml, refreshIcons } from './icons.js';
+
+var GITLAB_RESERVED = { admin: true, dashboard: true, explore: true, groups: true, help: true, profile: true, projects: true, public: true, search: true, snippets: true, users: true };
+
+function parseTarget(href, provider) {
+  if (typeof href !== "string" || !href) return null;
+  var url;
+  try { url = new URL(href); } catch (e) { return null; }
+  if (url.protocol !== "https:" || url.hostname !== provider.host || url.port || url.username || url.password) return null;
+  if (url.pathname.indexOf("//") !== -1 || /%(?:2f|5c)/i.test(url.pathname)) return null;
+  var parts = url.pathname.split("/").filter(function (part) { return part !== ""; });
+  var repoParts = parts;
+  var resourceParts = [];
+  if (provider.name === "github") {
+    repoParts = parts.slice(0, 2); resourceParts = parts.slice(2);
+  } else if (provider.separator) {
+    var separator = parts.indexOf(provider.separator);
+    if (separator !== -1) { repoParts = parts.slice(0, separator); resourceParts = parts.slice(separator + 1); }
+  }
+  if (repoParts.length < 2 || (provider.reserved && provider.reserved[repoParts[0].toLowerCase()])) return null;
+  if (provider.ownerPattern && !provider.ownerPattern.test(repoParts[0])) return null;
+  if (provider.repoPattern && !provider.repoPattern.test(repoParts[repoParts.length - 1])) return null;
+  for (var i = 0; i < repoParts.length; i++) {
+    if (!/^[A-Za-z0-9](?:[A-Za-z0-9._-]{0,99})$/.test(repoParts[i])) return null;
+  }
+  if (provider.name === "github" && repoParts.length !== 2) return null;
+  if (provider.name === "gitlab" && resourceParts.length > 2) return null;
+  var target = { url: url, provider: provider.name, icon: provider.icon, cssClass: provider.cssClass, owner: repoParts.slice(0, -1).join("/"), repo: repoParts[repoParts.length - 1], kind: "repository", label: repoParts.join("/") };
+  if (!resourceParts.length) return target;
+  if (provider.name === "github") {
+    if (resourceParts.length === 1 && (resourceParts[0] === "issues" || resourceParts[0] === "pulls")) {
+      target.kind = resourceParts[0]; target.label = resourceParts[0] === "issues" ? "Issues" : "Pull requests"; return target;
+    }
+    if (resourceParts.length === 2 && (resourceParts[0] === "issues" || resourceParts[0] === "pull") && /^\d+$/.test(resourceParts[1])) {
+      target.kind = resourceParts[0] === "pull" ? "pull" : "issue"; target.number = resourceParts[1]; target.label = target.kind === "pull" ? "PR #" + target.number : "Issue #" + target.number; return target;
+    }
+    return null;
+  }
+  if (resourceParts.length === 1 && (resourceParts[0] === "issues" || resourceParts[0] === "merge_requests")) {
+    target.kind = resourceParts[0] === "issues" ? "issues" : "merge_requests"; target.label = target.kind === "issues" ? "Issues" : "Merge requests"; return target;
+  }
+  if (resourceParts.length === 2 && (resourceParts[0] === "issues" || resourceParts[0] === "merge_requests") && /^\d+$/.test(resourceParts[1])) {
+    target.kind = resourceParts[0] === "issues" ? "issue" : "merge_request"; target.number = resourceParts[1]; target.label = target.kind === "issue" ? "Issue #" + target.number : "MR !" + target.number; return target;
+  }
+  return null;
+}
+
+var GITHUB = { name: "github", displayName: "GitHub", host: "github.com", icon: "github", cssClass: "github-link-chip", ownerPattern: /^[A-Za-z0-9](?:[A-Za-z0-9-]{0,38})$/, repoPattern: /^[A-Za-z0-9](?:[A-Za-z0-9._-]{0,99})$/ };
+var GITLAB = { name: "gitlab", displayName: "GitLab", host: "gitlab.com", icon: "gitlab", cssClass: "gitlab-link-chip", separator: "-", reserved: GITLAB_RESERVED };
+
+function plainLabel(text) {
+  return String(text || "").replace(/<[^>]*>/g, "").replace(/&amp;/g, "&").replace(/&lt;/g, "<").replace(/&gt;/g, ">").replace(/&quot;/g, '"').replace(/&#39;/g, "'").replace(/\s+/g, " ").trim();
+}
+
+function hasCustomLabel(target, text) {
+  var label = plainLabel(text);
+  return !!label && label !== target.url.href;
+}
+
+function accessibleLabel(target, text) {
+  var location = target.owner + "/" + target.repo;
+  var detail = target.kind === "repository" ? "" : " · " + target.label;
+  return hasCustomLabel(target, text) ? plainLabel(text) + " · " + location + detail : location + detail;
+}
+
+function chipMarkup(target, text) {
+  var custom = hasCustomLabel(target, text);
+  var primary = custom ? plainLabel(text) : target.owner + "/" + target.repo;
+  var meta = custom ? target.owner + "/" + target.repo + (target.kind === "repository" ? "" : " · " + target.label) : (target.kind === "repository" ? "" : target.label);
+  return iconHtml(target.icon, "github-link-icon") + '<span class="github-link-main">' + escapeHtml(primary) + '</span>' +
+    (meta && primary !== target.label ? '<span class="github-link-kind">' + escapeHtml(meta) + '</span>' : "");
+}
+
+function renderHostedLink(href, title, text, provider) {
+  var target = parseTarget(href, provider);
+  if (!target) return null;
+  return '<a class="' + provider.cssClass + ' hosted-link-chip" href="' + escapeHtml(target.url.href) + '" target="_blank" rel="noopener noreferrer"' +
+    (title ? ' title="' + escapeHtml(title) + '"' : ' title="Open ' + escapeHtml(accessibleLabel(target, text)) + ' on ' + provider.displayName + '"') +
+    ' aria-label="Open ' + escapeHtml(accessibleLabel(target, text)) + ' on ' + provider.displayName + '">' + chipMarkup(target, text) + '</a>';
+}
+
+export function githubLinkTarget(href) {
+  var target = parseTarget(href, GITHUB);
+  if (!target) return null;
+  return { owner: target.owner, repo: target.repo, kind: target.kind, number: target.number || null, href: target.url.href, label: target.label };
+}
+
+export function gitlabLinkTarget(href) {
+  var target = parseTarget(href, GITLAB);
+  if (!target) return null;
+  return { owner: target.owner, repo: target.repo, kind: target.kind, number: target.number || null, href: target.url.href, label: target.label };
+}
+
+export function renderGithubLink(href, title, text) { return renderHostedLink(href, title, text, GITHUB); }
+export function renderGitlabLink(href, title, text) { return renderHostedLink(href, title, text, GITLAB); }
+
+export function enhanceGithubLinks(root) {
+  if (!root || typeof document === "undefined") return;
+  var anchors = root.querySelectorAll("a[href]");
+  for (var i = 0; i < anchors.length; i++) {
+    var anchor = anchors[i];
+    if (anchor.closest("code, pre")) continue;
+    var target = parseTarget(anchor.getAttribute("href"), anchor.classList.contains("gitlab-link-chip") ? GITLAB : GITHUB);
+    if (!target) { target = parseTarget(anchor.getAttribute("href"), GITLAB); if (!target) continue; }
+    var text = anchor.textContent || "";
+    if (anchor.classList.contains("github-link-chip") || anchor.classList.contains("gitlab-link-chip")) {
+      anchor.setAttribute("target", "_blank"); anchor.setAttribute("rel", "noopener noreferrer"); continue;
+    }
+    anchor.classList.add("hosted-link-chip", target.cssClass); anchor.setAttribute("target", "_blank"); anchor.setAttribute("rel", "noopener noreferrer");
+    anchor.setAttribute("aria-label", "Open " + accessibleLabel(target, text) + " on " + (target.provider === "gitlab" ? "GitLab" : "GitHub"));
+    anchor.innerHTML = chipMarkup(target, text);
+  }
+  refreshIcons();
+}

package/lib/public/modules/markdown.js

@@ -4,6 +4,7 @@ import { getMermaidThemeVars } from './theme.js';
 import { store } from './store.js';
 import { enhanceClayLogLinks, renderClayRecordLink } from './clay-log-links.js';
 import { renderLocalFileLink, enhanceClayFileLinks } from './clay-file-links.js';
+import { renderGithubLink, renderGitlabLink } from './github-links.js';
 
 // Initialize markdown parser
 marked.use({ gfm: true, breaks: false });
@@ -11,11 +12,17 @@ marked.use({ gfm: true, breaks: false });
 // Open external links in a new tab
 marked.use({
   renderer: {
-    link({ href, title, text }) {
+    link({ href, title, tokens, text }) {
       var recordLink = renderClayRecordLink(href, text);
       if (recordLink) return recordLink;
       var localLink = renderLocalFileLink(href, title, text);
       if (localLink) return localLink;
+      var githubText = text;
+      if (tokens && this.parser && this.parser.parseInline) githubText = this.parser.parseInline(tokens);
+      var githubLink = renderGithubLink(href, title, githubText);
+      if (githubLink) return githubLink;
+      var gitlabLink = renderGitlabLink(href, title, githubText);
+      if (gitlabLink) return gitlabLink;
       var isExternal = href && (href.startsWith('http://') || href.startsWith('https://'));
       var titleAttr = title ? ' title="' + title + '"' : '';
       var targetAttr = isExternal ? ' target="_blank" rel="noopener noreferrer"' : '';
@@ -56,7 +63,7 @@ export function renderMarkdown(text) {
     .replace(/[\u201C\u201D]/g, '"')
     .replace(/[\u2018\u2019]/g, "'")
     .replace(/\*\*[ \t]+([^*\n]+?)[ \t]+\*\*/g, "**$1**"));
-  return DOMPurify.sanitize(marked.parse(normalized));
+  return DOMPurify.sanitize(marked.parse(normalized), { ADD_ATTR: ["target", "rel"] });
 }
 
 export function enhanceClaySessionLinks(root) {

package/lib/public/modules/mcp-ui.js

@@ -4,6 +4,8 @@
 import { getWs } from './ws-ref.js';
 import { refreshIcons } from './icons.js';
 import { setHttpMcpServers } from './app-misc.js';
+import { store } from './store.js';
+import { showToast } from './utils.js';
 
 var modal = null;
 var contentEl = null;
@@ -11,6 +13,60 @@ var _mcpServers = []; // { name, transport, toolCount, extensionEnabled, project
 var _extensionConnected = false;
 var _nativeHostConnected = false;
 var _extensionId = null;
+var MCP_PERMISSION_TIMEOUT_MS = 10000;
+var _permissionModeTimers = {};
+
+function pendingKey(projectSlug, sessionId, requestId) {
+  return String(projectSlug) + ":" + String(sessionId) + ":" + String(requestId);
+}
+
+function pendingMap() {
+  return store.get('mcpPermissionModePendingByTarget') || {};
+}
+
+function setPendingMap(next) {
+  store.set({ mcpPermissionModePendingByTarget: next });
+}
+
+function findPending(requestId) {
+  var pending = pendingMap();
+  var keys = Object.keys(pending);
+  for (var i = 0; i < keys.length; i++) {
+    if (pending[keys[i]].requestId === requestId) return { key: keys[i], value: pending[keys[i]] };
+  }
+  return null;
+}
+
+function clearPendingRequest(requestId) {
+  var found = findPending(requestId);
+  if (!found) return null;
+  if (_permissionModeTimers[requestId]) clearTimeout(_permissionModeTimers[requestId]);
+  delete _permissionModeTimers[requestId];
+  var next = Object.assign({}, pendingMap());
+  delete next[found.key];
+  setPendingMap(next);
+  return found.value;
+}
+
+export function clearMcpPermissionModePending() {
+  var requestIds = Object.keys(_permissionModeTimers);
+  for (var i = 0; i < requestIds.length; i++) clearTimeout(_permissionModeTimers[requestIds[i]]);
+  _permissionModeTimers = {};
+  if (Object.keys(pendingMap()).length) setPendingMap({});
+}
+
+export function mcpPermissionModeApplicability(state) {
+  if (!state.permissionCapabilities || state.permissionCapabilities.mcpOverride !== true) {
+    return { applicable: false, reason: "AI review is unavailable for this SDK session." };
+  }
+  if (state.effectivePermissionMode === "auto" || state.effectivePermissionMode === "bypassPermissions") {
+    return { applicable: true, reason: "" };
+  }
+  if (!state.effectivePermissionMode && state.currentMode === "auto") {
+    return { applicable: false, reason: "Waiting for the SDK to confirm Auto." };
+  }
+  return { applicable: false, reason: "AI review requires an active Auto session." };
+}
 
 export function initMcp() {
   modal = document.getElementById("mcp-modal");
@@ -26,6 +82,14 @@ export function initMcp() {
   if (closeBtn) closeBtn.addEventListener("click", closeMcpModal);
   if (backdrop) backdrop.addEventListener("click", closeMcpModal);
 
+  store.subscribe(function (state, prev) {
+    var changed = state.activeSessionId !== prev.activeSessionId || state.currentSlug !== prev.currentSlug ||
+      state.currentMode !== prev.currentMode || state.effectivePermissionMode !== prev.effectivePermissionMode ||
+      state.permissionCapabilities !== prev.permissionCapabilities || state.mcpPermissionModeOverrides !== prev.mcpPermissionModeOverrides ||
+      state.mcpPermissionModePendingByTarget !== prev.mcpPermissionModePendingByTarget || state.connected !== prev.connected;
+    if (changed && modal && !modal.classList.contains("hidden")) renderMcpServerList();
+  });
+
   // ESC to close
   document.addEventListener("keydown", function (e) {
     if (e.key === "Escape" && modal && !modal.classList.contains("hidden")) {
@@ -140,21 +204,47 @@ function renderMcpServerList() {
 
       // Per-server permission mode override (applies to the active session only).
       if (server.projectEnabled) {
+        var permissionState = store.snap();
+        var applicability = mcpPermissionModeApplicability(permissionState);
+        if (!applicability.applicable) {
+          var unavailable = document.createElement("span");
+          unavailable.className = "mcp-server-perm-reason";
+          unavailable.textContent = applicability.reason;
+          row.appendChild(unavailable);
+          contentEl.appendChild(row);
+          continue;
+        }
         var modeSel = document.createElement("select");
         modeSel.className = "mcp-server-perm-mode";
         modeSel.dataset.serverName = server.name;
-        modeSel.title = "Permission mode for this server (this session only)";
+        modeSel.title = "AI review policy for this server (this session only)";
+        var optInherit = document.createElement("option");
+        optInherit.value = "";
+        optInherit.textContent = "Inherit";
         var optAsk = document.createElement("option");
         optAsk.value = "default";
         optAsk.textContent = "Ask";
         var optAuto = document.createElement("option");
         optAuto.value = "auto";
-        optAuto.textContent = "Auto-approve";
+        optAuto.textContent = "AI review";
+        modeSel.appendChild(optInherit);
         modeSel.appendChild(optAsk);
         modeSel.appendChild(optAuto);
-        modeSel.value = server.permissionModeOverride === "auto" ? "auto" : "default";
+        var overrides = store.get('mcpPermissionModeOverrides') || {};
+        modeSel.value = overrides[server.name] === "auto" || overrides[server.name] === "default" ? overrides[server.name] : "";
+        var pending = pendingMap();
+        var pendingKeys = Object.keys(pending);
+        for (var p = 0; p < pendingKeys.length; p++) {
+          var pendingValue = pending[pendingKeys[p]];
+          if (pendingValue.projectSlug === permissionState.currentSlug && pendingValue.sessionId === permissionState.activeSessionId && pendingValue.serverName === server.name) {
+            modeSel.value = pendingValue.mode;
+            modeSel.disabled = true;
+            break;
+          }
+        }
+        if (!permissionState.connected) modeSel.disabled = true;
         // The row is a <label>; keep select interactions from toggling the checkbox.
-        modeSel.addEventListener("click", function (e) { e.stopPropagation(); e.preventDefault(); });
+        modeSel.addEventListener("click", function (e) { e.stopPropagation(); });
         modeSel.addEventListener("change", onPermissionModeChange);
         row.appendChild(modeSel);
       }
@@ -318,22 +408,69 @@ function onToggle(e) {
 
 function onPermissionModeChange(e) {
   var name = e.target.dataset.serverName;
-  var mode = e.target.value; // "default" | "auto"
-
-  // Remember locally so a re-render keeps the selection.
-  for (var i = 0; i < _mcpServers.length; i++) {
-    if (_mcpServers[i].name === name) {
-      _mcpServers[i].permissionModeOverride = mode;
-      break;
-    }
-  }
+  sendMcpPermissionMode(store.get('currentSlug'), store.get('activeSessionId'), name, e.target.value);
+}
 
+export function sendMcpPermissionMode(projectSlug, sessionId, serverName, mode) {
+  var state = store.snap();
+  var applicability = mcpPermissionModeApplicability(state);
   var ws = getWs();
-  if (ws && ws.readyState === 1) {
-    ws.send(JSON.stringify({
+  if (!state.connected || state.currentSlug !== projectSlug || state.activeSessionId !== sessionId || !applicability.applicable || !ws || ws.readyState !== 1) {
+    showToast(applicability.applicable ? "Reconnect before changing AI review policy." : applicability.reason, "error");
+    return false;
+  }
+  var pending = pendingMap();
+  var pendingKeys = Object.keys(pending);
+  for (var i = 0; i < pendingKeys.length; i++) {
+    var item = pending[pendingKeys[i]];
+    if (item.projectSlug === projectSlug && item.sessionId === sessionId && item.serverName === serverName) return false;
+  }
+  var requestId = typeof crypto !== "undefined" && crypto.randomUUID ? crypto.randomUUID() : String(Date.now());
+  var key = pendingKey(projectSlug, sessionId, requestId);
+  var overrides = state.mcpPermissionModeOverrides || {};
+  var next = Object.assign({}, pending);
+  next[key] = {
+    projectSlug: projectSlug,
+    sessionId: sessionId,
+    requestId: requestId,
+    serverName: serverName,
+    mode: mode || "",
+    previousMode: overrides[serverName] || ""
+  };
+  setPendingMap(next);
+  _permissionModeTimers[requestId] = setTimeout(function () {
+    if (!clearPendingRequest(requestId)) return;
+    showToast("Changing AI review policy timed out.", "error");
+  }, MCP_PERMISSION_TIMEOUT_MS);
+  try {
+    var result = ws.send(JSON.stringify({
       type: "set_mcp_permission_mode_override",
-      serverName: name,
-      mode: mode,
+      projectSlug: projectSlug,
+      sessionId: sessionId,
+      requestId: requestId,
+      serverName: serverName,
+      mode: mode || null,
     }));
+    if (result === false) throw new Error("WebSocket send failed");
+  } catch (error) {
+    clearPendingRequest(requestId);
+    showToast("Failed to send the AI review policy change.", "error");
+    return false;
+  }
+  return true;
+}
+
+export function handleMcpPermissionModeResult(msg) {
+  var found = findPending(msg.requestId);
+  if (!found) return;
+  var pending = found.value;
+  if (msg.projectSlug && msg.projectSlug !== pending.projectSlug) return;
+  if (msg.sessionId !== pending.sessionId || msg.serverName !== pending.serverName) return;
+  clearPendingRequest(msg.requestId);
+  if (pending.projectSlug !== store.get('currentSlug') || pending.sessionId !== store.get('activeSessionId')) return;
+  if (!msg.ok) {
+    showToast(msg.error || "Failed to change AI review policy.", "error");
+    return;
   }
+  store.set({ mcpPermissionModeOverrides: msg.mcpPermissionModeOverrides || {} });
 }