clay-server 4.1.0 → 4.2.0-beta.2

package/lib/public/css/command-palette.css

@@ -512,9 +512,45 @@ body.mate-dm-active .search-clay-transcript .search-clay-message-user .bubble,
 .search-clay-activity-item small { color: var(--text-dimmer); font-size: 10px; line-height: 1.35; }
 @keyframes searchClaySpin { to { transform: rotate(360deg); } }
 
-.clayos-session-link,
-.clayos-issue-link,
-.clayos-log-link {
+.clayos-record-link {
+  display: inline-flex;
+  align-items: center;
+  gap: 6px;
+  min-height: 28px;
+  margin: 2px 1px;
+  padding: 3px 8px 3px 6px;
+  border: 1px solid color-mix(in srgb, var(--record-color, var(--accent)) 32%, var(--border));
+  border-radius: 8px;
+  background: color-mix(in srgb, var(--record-color, var(--accent)) 7%, var(--bg-alt));
+  color: var(--text);
+  font: inherit;
+  font-size: 11px;
+  line-height: 1;
+  vertical-align: middle;
+  cursor: pointer;
+}
+.clayos-record-link::before {
+  content: "\2197";
+  display: grid;
+  place-items: center;
+  width: 17px;
+  height: 17px;
+  border-radius: 5px;
+  background: color-mix(in srgb, var(--record-color, var(--accent)) 14%, transparent);
+  color: var(--record-color, var(--accent));
+  font-size: 12px;
+}
+.clayos-record-link > span { font-weight: 620; }
+.clayos-record-link > small { min-width: 0; max-width: 28em; overflow: hidden; text-overflow: ellipsis; white-space: nowrap; border-inline-start: 1px solid color-mix(in srgb, currentColor 22%, transparent); padding-inline-start: 6px; color: var(--text-muted); font-size: 11px; }
+.clayos-record-link:hover { border-color: color-mix(in srgb, var(--record-color, var(--accent)) 58%, var(--border)); background: color-mix(in srgb, var(--record-color, var(--accent)) 11%, var(--bg-alt)); }
+.clayos-record-link:focus-visible { outline: 2px solid var(--record-color, var(--accent)); outline-offset: 2px; }
+.clayos-record-link.is-loading { opacity: 0.62; cursor: progress; }
+.clayos-record-link.is-loading::before { animation: searchClaySpin 1.2s linear infinite; }
+.clayos-record-link.is-error { border-color: color-mix(in srgb, var(--warning) 48%, var(--border)); }
+.clayos-issue-link { --record-color: var(--link, var(--accent)); }
+.clayos-log-link { --record-color: var(--accent); }
+
+.clayos-session-link {
   display: inline-flex;
   align-items: center;
   gap: 6px;
@@ -531,9 +567,7 @@ body.mate-dm-active .search-clay-transcript .search-clay-message-user .bubble,
   vertical-align: middle;
   cursor: pointer;
 }
-.clayos-session-link::before,
-.clayos-issue-link::before,
-.clayos-log-link::before {
+.clayos-session-link::before {
   content: "\2197";
   display: grid;
   place-items: center;
@@ -544,29 +578,13 @@ body.mate-dm-active .search-clay-transcript .search-clay-message-user .bubble,
   color: var(--accent);
   font-size: 12px;
 }
-.clayos-issue-link::before,
-.clayos-log-link::before { content: "\2261"; }
-.clayos-session-link > span,
-.clayos-issue-link > span,
-.clayos-log-link > span { font-weight: 620; }
-.clayos-session-link > small,
-.clayos-issue-link > small,
-.clayos-log-link > small { color: var(--text-muted); font-size: 10px; }
-.clayos-session-link:hover,
-.clayos-issue-link:hover,
-.clayos-log-link:hover { border-color: color-mix(in srgb, var(--accent) 52%, var(--border)); background: color-mix(in srgb, var(--accent) 11%, var(--bg-alt)); }
-.clayos-session-link:focus-visible,
-.clayos-issue-link:focus-visible,
-.clayos-log-link:focus-visible { outline: 2px solid var(--accent); outline-offset: 2px; }
-.clayos-session-link.is-loading,
-.clayos-issue-link.is-loading,
-.clayos-log-link.is-loading { opacity: 0.62; cursor: progress; }
-.clayos-session-link.is-loading::before,
-.clayos-issue-link.is-loading::before,
-.clayos-log-link.is-loading::before { animation: searchClaySpin 1.2s linear infinite; }
-.clayos-session-link.is-error,
-.clayos-issue-link.is-error,
-.clayos-log-link.is-error { border-color: color-mix(in srgb, var(--warning) 48%, var(--border)); }
+.clayos-session-link > span { font-weight: 620; }
+.clayos-session-link > small { color: var(--text-muted); font-size: 10px; }
+.clayos-session-link:hover { border-color: color-mix(in srgb, var(--accent) 52%, var(--border)); background: color-mix(in srgb, var(--accent) 11%, var(--bg-alt)); }
+.clayos-session-link:focus-visible { outline: 2px solid var(--accent); outline-offset: 2px; }
+.clayos-session-link.is-loading { opacity: 0.62; cursor: progress; }
+.clayos-session-link.is-loading::before { animation: searchClaySpin 1.2s linear infinite; }
+.clayos-session-link.is-error { border-color: color-mix(in srgb, var(--warning) 48%, var(--border)); }
 
 .search-clay-pending {
   align-self: flex-start;
@@ -925,11 +943,11 @@ body.mate-dm-active .search-clay-transcript .search-clay-message-user .bubble,
 }
 
 .clayos-issue-link { max-width: min(100%, 30em); box-sizing: border-box; }
+.clayos-issue-link::before,
+.clayos-log-link::before { content: "\2261"; }
 .clayos-issue-link::before { content: "\25CE"; flex: 0 0 17px; }
-.clayos-issue-link[data-status="in_progress"]::before { color: #bd923f; }
-.clayos-issue-link[data-status="resolved"]::before { content: "\2713"; color: var(--brand-green); }
+.clayos-issue-link[data-status="in_progress"]::before { color: var(--warning, var(--accent)); }
+.clayos-issue-link[data-status="resolved"]::before { content: "\2713"; color: var(--success, var(--accent)); }
 .clayos-issue-link[data-status="closed"]::before { content: "\00D7"; color: var(--text-dimmer); }
 .clayos-issue-link > span { flex-shrink: 0; }
-.clayos-issue-link > small { min-width: 0; overflow: hidden; white-space: nowrap; text-overflow: ellipsis; }
 .clayos-log-link { max-width: 100%; box-sizing: border-box; }
-.clayos-log-link > small { min-width: 0; overflow-wrap: anywhere; line-height: 1.35; }

package/lib/public/css/filebrowser.css

@@ -686,6 +686,26 @@
   font-size: 12px;
   color: var(--text-muted);
 }
+.mcp-server-perm-mode {
+  max-width: 118px;
+  padding: 5px 24px 5px 8px;
+  border: 1px solid var(--border);
+  border-radius: 6px;
+  background: var(--bg);
+  color: var(--text);
+  font-size: 12px;
+}
+.mcp-server-perm-mode:disabled {
+  cursor: wait;
+  opacity: 0.55;
+}
+.mcp-server-perm-reason {
+  max-width: 180px;
+  color: var(--text-muted);
+  font-size: 11px;
+  line-height: 1.3;
+  text-align: right;
+}
 
 /* Beta toggle row inside settings card */
 .ps-beta-toggle-row,

package/lib/public/css/issues.css

@@ -46,11 +46,11 @@
 .issue-row small { font-size: 10.5px; font-family: var(--font-mono); }
 .issue-row-meta { display: flex; align-items: baseline; flex-wrap: wrap; gap: 8px; margin-top: 8px; color: var(--text-dimmer); font: 10.5px/1.5 var(--font-mono); }
 .issue-row-meta .issue-status { font-family: var(--font-sans); }
-.issue-status { display: inline-flex; align-items: center; gap: 6px; font-size: 11px; letter-spacing: .03em; }
+.issue-status { display: inline-flex; align-items: center; gap: 6px; color: var(--text-secondary); font-size: 11px; letter-spacing: .03em; }
 .issue-status::before { content: ''; width: 7px; height: 7px; border: 1px solid currentColor; border-radius: 50%; }
-.issue-status[data-status="in_progress"] { color: #bd923f; }
-.issue-status[data-status="resolved"] { color: #479b77; }
-.issue-status[data-status="closed"] { color: var(--text-muted); }
+.issue-status[data-status="in_progress"]::before { color: var(--warning, var(--accent)); }
+.issue-status[data-status="resolved"]::before { color: var(--success, var(--accent)); }
+.issue-status[data-status="closed"]::before { color: var(--text-muted); }
 .issue-detail { max-width: 760px; margin: 0 auto; padding: 32px 28px 52px; }
 .issue-doc-chips { display: flex; align-items: center; flex-wrap: wrap; gap: 7px; margin-bottom: 10px; }
 .issue-detail .issue-doc-title { margin: 0 0 10px; font-family: var(--font-display); font-size: clamp(24px, 2.8vw, 34px); letter-spacing: -.025em; line-height: 1.12; overflow-wrap: anywhere; }

package/lib/public/css/messages.css

@@ -508,6 +508,33 @@ pre:hover .code-copy-btn { opacity: 1; }
 .clay-file-link-label { min-width: 0; overflow: hidden; text-overflow: ellipsis; white-space: nowrap; }
 .clay-file-link-notice { margin-top: 5px; color: var(--text-secondary); font-size: 12px; }
 
+.hosted-link-chip, .github-link-chip {
+  display: inline-flex;
+  align-items: center;
+  gap: 5px;
+  max-width: 100%;
+  padding: 3px 8px;
+  border: 1px solid color-mix(in srgb, var(--text) 16%, var(--border));
+  border-radius: 999px;
+  background: color-mix(in srgb, var(--text) 8%, var(--bg));
+  color: var(--text);
+  font-size: 0.92em;
+  line-height: 1.35;
+  vertical-align: baseline;
+  text-decoration: none !important;
+  transition: background 120ms ease, border-color 120ms ease, transform 120ms ease;
+}
+.hosted-link-chip { color: var(--text); }
+.md-content .github-link-chip { color: var(--text); }
+.md-content .gitlab-link-chip { color: var(--text); }
+.hosted-link-chip:hover, .github-link-chip:hover { background: color-mix(in srgb, var(--text) 14%, var(--bg-alt)); border-color: color-mix(in srgb, var(--text) 30%, var(--border)); }
+.hosted-link-chip:active, .github-link-chip:active { transform: translateY(1px); }
+.hosted-link-chip:focus-visible, .github-link-chip:focus-visible { outline: 2px solid var(--link); outline-offset: 2px; }
+.github-link-icon { display: inline-flex; width: 15px; height: 15px; flex: 0 0 15px; }
+.github-link-icon .lucide { width: 15px; height: 15px; }
+.github-link-main { min-width: 0; overflow: hidden; text-overflow: ellipsis; white-space: nowrap; }
+.github-link-kind { min-width: 0; max-width: 65%; flex: 0 1 auto; overflow: hidden; text-overflow: ellipsis; white-space: nowrap; color: var(--text-muted); font-size: 0.88em; }
+
 .md-content ul, .md-content ol {
   padding-left: 24px;
   margin: 10px 0;

package/lib/public/css/overlays.css

@@ -519,6 +519,66 @@ button.top-bar-pill.pill-accent:hover { background: color-mix(in srgb, var(--acc
 .popover-copy.copied { color: var(--success); border-color: var(--success); }
 
 /* Skip permissions pill */
+.session-permission-control {
+  display: inline-flex;
+  align-items: center;
+  flex: 0 1 auto;
+  flex-wrap: wrap;
+  gap: 7px;
+  max-width: 100%;
+  min-width: 0;
+}
+.session-permission-control.hidden { display: none; }
+.session-permission-segmented {
+  display: inline-flex;
+  align-items: center;
+  flex: 0 0 auto;
+  gap: 2px;
+  padding: 2px;
+  border: 1px solid var(--border, rgba(255,255,255,.18));
+  border-radius: 999px;
+  background: var(--surface-raised, rgba(0,0,0,.18));
+}
+.session-permission-segmented button {
+  flex: 0 0 auto;
+  border: 0;
+  border-radius: 999px;
+  padding: 3px 8px;
+  color: var(--text-muted, inherit);
+  background: transparent;
+  font: inherit;
+  font-size: 11px;
+  white-space: nowrap;
+  cursor: pointer;
+}
+.session-permission-segmented button.active { background: var(--accent, #6f8cff); color: #fff; }
+.session-permission-segmented button:disabled { cursor: not-allowed; opacity: .5; }
+.session-permission-control.permission-pending .session-permission-segmented button:disabled { cursor: wait; }
+.session-permission-status {
+  flex: 1 1 118px;
+  min-width: 0;
+  max-width: 190px;
+  overflow-wrap: anywhere;
+  white-space: normal;
+  color: var(--text-dimmer, var(--text-muted));
+  font-size: 10px;
+  line-height: 1.2;
+}
+.session-permission-status.hidden { display: none; }
+.permission-runtime-fallback .session-permission-status { color: var(--warning, #d49a55); }
+.permission-globally-forced .session-permission-status { color: var(--warning, #d49a55); }
+.permission-label-short { display: none; }
+@media (max-width: 760px) {
+  .permission-label-long { display: none; }
+  .permission-label-short { display: inline; }
+  .session-permission-control { column-gap: 5px; row-gap: 2px; }
+  .session-permission-segmented button { padding-inline: 7px; }
+  .session-permission-status {
+    flex-basis: 96px;
+    max-width: 170px;
+    font-size: 9px;
+  }
+}
 #skip-perms-pill .lucide { width: 12px; height: 12px; flex-shrink: 0; }
 
 /* --- Confirm modal --- */

package/lib/public/css/pane.css

@@ -370,13 +370,31 @@ body.pane-mode #input-area {
    tie and keep the pill at its 22px title-bar size inside the 24px pane
    header. Scope under .split-pane-header to outrank them. */
 .split-pane-header .split-pane-full-access {
-  height: 15px;
+  height: auto;
   align-self: center;
   margin-left: 0;
-  padding: 0 3px 0 7px;
-  gap: 5px;
+  padding: 0;
+  gap: 4px;
   font-size: 8px;
   letter-spacing: 0.02em;
+  flex-wrap: nowrap;
+  flex: 0 0 auto;
+  overflow: hidden;
+}
+
+.split-pane-header .session-permission-segmented button {
+  padding: 1px 5px;
+  font-size: 8px;
+}
+
+.split-pane-header .session-permission-status {
+  flex: 0 0 auto;
+  min-width: 40px;
+  max-width: 72px;
+  overflow: hidden;
+  text-overflow: ellipsis;
+  white-space: nowrap;
+  font-size: 8px;
 }
 
 .split-pane-header .session-full-access-track {
@@ -395,7 +413,6 @@ body.pane-mode #input-area {
 
 @media (max-width: 900px) {
   .split-pane-header .session-full-access-label { display: none; }
-  .split-pane-header .split-pane-full-access { padding-left: 3px; }
 }
 
 .split-pane-close {

package/lib/public/css/pending-message-queue.css

@@ -167,6 +167,11 @@ button.pending-message-drag:active { cursor: grabbing; }
 .pending-message-banner-error { color: var(--error); font-size: 10px; line-height: 1.35; }
 .pending-message-error { margin-top: 4px; }
 .pending-message-banner-error { padding: 0 8px 6px; }
+.pending-message-restoring { padding: 0 8px 6px; color: var(--text-dimmer); font-size: 10px; line-height: 1.35; }
+
+.pending-message-drag:disabled,
+.pending-message-actions button:disabled,
+.pending-message-resume:disabled { cursor: not-allowed; opacity: .48; }
 
 .pending-message-drag:focus-visible,
 .pending-message-actions button:focus-visible,

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="">
@@ -830,6 +835,16 @@
                   </div>
                 </div>
               </div>
+              <div class="settings-field" id="ps-session-visibility-default-field" style="display:none">
+                <label class="settings-label" for="ps-session-visibility-default">New session visibility</label>
+                <div class="settings-hint">Applies to new project conversations and Issue Start work sessions. Existing sessions, hidden work, and delegated workflows keep their current visibility.</div>
+                <div class="settings-hint hidden" id="ps-session-visibility-default-inherited-hint">This worktree inherits the setting from its parent project. Change it there.</div>
+                <div class="settings-hint hidden" id="ps-session-visibility-default-non-current-hint">Open this project to change this setting.</div>
+                <select class="ps-select" id="ps-session-visibility-default">
+                  <option value="private">Private</option>
+                  <option value="shared">Shared with project members</option>
+                </select>
+              </div>
             </div>
           </div>
           <!-- Defaults -->

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

@@ -38,6 +38,7 @@ import { handleFsList, handleFsRead, handleFileChanged, handleDirChanged, handle
 import { beginMarkdownTurn, finishMarkdownTurn, markdownPathFromToolInput } from './markdown-live-edit.js';
 import { forwardPaneMarkdownPresentation } from './pane-bridge.js';
 import { isProjectSettingsOpen, handleInstructionsRead, handleInstructionsWrite, handleProjectEnv, handleProjectEnvSaved, handleProjectSharedEnv, handleProjectSharedEnvSaved, handleProjectOwnerChanged } from './project-settings.js';
+import { handleProjectSessionVisibilityDefault, refreshProjectSessionVisibilitySettings } from './project-session-visibility-settings.js';
 import { updateSettingsStats, updateDaemonConfig, handleSetPinResult, handleKeepAwakeChanged, handleInheritGroupsChanged, handleAutoContinueChanged, handleRestartResult, handleShutdownResult, handleSharedEnv, handleSharedEnvSaved, handleGlobalClaudeMdRead, handleGlobalClaudeMdWrite } from './server-settings.js';
 import { handleTermList, handleTermCreated, sendTerminalCommand, handleTermOutput, handleTermResized, handleTermExited, handleTermClosed } from './terminal.js';
 import { attachTuiView, detachTuiView, setTuiSuspendedView, tuiHandleTermOutput, tuiHandleTermResized, tuiHandleTermExited, tuiHandleTermClosed } from './session-tui-view.js';
@@ -53,7 +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';
@@ -103,6 +105,10 @@ export function processMessage(msg) {
   if (handleScheduledTaskMessage(msg)) return;
   if (handleDefaultVendorMessage(msg)) return;
   if (handleContextViewMessage(msg)) return;
+  if (msg && msg.type === "set_project_session_visibility_default_result") {
+    handleProjectSessionVisibilityDefault(msg);
+    return;
+  }
   if (msg && msg.type === "schedule_message_result") {
     handleScheduleMessageResult(msg);
     return;
@@ -369,12 +375,11 @@ 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;
 
       case "update_available":
@@ -549,6 +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;
@@ -817,7 +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);
@@ -1592,6 +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.
@@ -1735,6 +1751,7 @@ export function processMessage(msg) {
 
       case "projects_updated":
         updateProjectList(msg);
+        refreshProjectSessionVisibilitySettings(msg.projects);
         renderUserStrip();
         break;
 

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-issue-links.js

@@ -31,6 +31,7 @@ function createIssueLink(ref, labelText) {
   var button = document.createElement("button");
   button.type = "button";
   button.className = "clayos-issue-link";
+  button.classList.add("clayos-record-link");
   button.contentEditable = "false";
   button.dataset.issueRef = ref;
   button.setAttribute("aria-label", "Open Project Issue" + (labelText ? " " + labelText : ""));