mixdog 1.0.0 → 1.0.2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "mixdog",
-  "version": "1.0.0",
+  "version": "1.0.2",
   "private": false,
   "type": "module",
   "description": "Standalone mixdog coding-agent CLI/TUI workspace.",
@@ -31,7 +31,7 @@
     "!scripts/bench/",
     "!scripts/recall-bench-*.txt",
     "!scripts/*-test.mjs",
-    "!scripts/*.test.mjs",
+    "!scripts/**/*.test.mjs",
     "!scripts/tool-contracts/",
     "!scripts/provider-toolcall/",
     "!scripts/session-transport/",

package/src/defaults/skills/computer-use/SKILL.md

@@ -115,18 +115,19 @@ GNOME with the Window Calls extension); prefer accessibility refs there.
   of the shared desktop. If that surface is unavailable, use semantic refs or
   report `pixel_unavailable`; do not substitute a screen grab.
 - If the user intervenes, preserve their cursor and focus. Worker termination
-  and input cleanup must finish before resuming; a failed cleanup is not cleared
-  by a resume request. Ask the user to press `Ctrl+Alt+Esc`, or the overlay's
-  Stop control, for verified cleanup recovery.
-  If target-local release remains unconfirmed, the user must inspect/recover
-  that window; restarting the host alone does not prove release. Obtain a new
-  observation after an interruption.
-  Use `wait_for_user` to keep the task waiting without sending input. The host
-  may resume ordinary physical-input interruptions after its configured quiet
-  interval; renewed input resets that interval. Explicit pauses/stops and
-  uncertain observation/cleanup never auto-resume. The overlay's only control
-  is Stop, which cancels the task. Never operate it or the recovery controls,
-  or change the idle policy, on the user's behalf.
+  and input cleanup must finish before resuming. The user's Resume on the
+  overlay continues a pause; an ordinary physical-input pause may also resume
+  after the host's configured quiet interval (renewed input resets it), while
+  explicit pauses, stops and uncertain cleanup never auto-resume. Stop (or
+  `Ctrl+Alt+Esc`) cancels the task, which then reports the stop as a failure.
+  A cleanup that could not be confirmed is retried before the next input
+  command; if it still fails, that command returns the reason — relay it to
+  the user. If target-local release remains unconfirmed, the user must
+  inspect/recover that window; restarting the host alone does not prove
+  release. Obtain a new observation after an interruption.
+  Use `wait_for_user` to keep the task waiting without sending input. Never
+  operate Resume, Stop or the recovery controls, or change the idle policy, on
+  the user's behalf.
   While paused, only `list`, `diagnose` and `wait_for_user` are available.
   Chat text alone does not clear the host. After `resumed`, capture fresh state;
   after `timeout` or `cancelled`, no input is authorized. Never replay the

package/src/defaults/skills/setup/SKILL.md

@@ -25,7 +25,7 @@ supported `setup` action, and read its result as the change receipt.
   arguments and the transcript. Open the Providers surface and let the user
   enter them.
 - A mutation follows the active workflow's approval rules. Status, catalog,
-  definition, MCP-config and Instructions reads do not change persisted settings.
+  definition and MCP-config reads do not change persisted settings.
 - Most changes affect new sessions. Report `appliedToCurrentSession` and
   `appliesTo` exactly when the result supplies them.
 - This skill does not own source edits, builds, installation deployment,
@@ -78,9 +78,6 @@ that a call returned without transport error.
 - Read definitions before editing them; use skill-creator when authoring a
   skill. Setup persists the supported definition fields. Workflow and agent
   ids are stable identities, distinct from their display names.
-- Read Instructions before replacing them and pass the returned text as
-  `expectedContent`. `projectPath:null` means Common Instructions; otherwise
-  use an exact registered Project root. Keep the returned backup.
 - MCP servers and plugins are machine-global integrations whose visibility may
   be scoped to selected Projects.
 - User skills are machine-global. Enabled plugin skills and built-in skills are

package/src/defaults/skills/setup/references/actions.md

@@ -64,13 +64,11 @@ Read this when choosing a `setup` mutation.
 | Delete an existing schedule/webhook | `delete_automation` |
 | Enable/disable a schedule/webhook | `set_automation_enabled` |
 | Webhook listener enabled state, port, or domain | `set_webhook_config` |
-| Desktop keep-awake, usage pin, or Computer observe-only state | `set_desktop_settings` |
+| Desktop keep-awake, run in background after window close, usage pin, or Computer observe-only state | `set_desktop_settings` |
 | Desktop theme, display language, side panels, or zoom | `set_appearance` |
 | Register a Project and optionally set its display alias | `save_project` |
 | Unregister a Project without deleting its files | `remove_project` |
-| Read Project/Common Instructions before editing | `get_instructions` |
-| Replace unchanged Project/Common Instructions and retain a backup | `set_instructions` |
-| Revoke one linked device; re-pairing restores access | `revoke_linked_device` |
+| Revoke one linked device by its client id from `status connection`; re-pairing restores access | `revoke_linked_device` |
 | Managed local model context allocation; null restores automatic | `set_local_context` |
 
 ## Routes and workflow
@@ -118,7 +116,10 @@ values through chat.
 ## Built-in features
 
 Read `status features` and distinguish installation, enabled state, and live
-bridge state.
+bridge state. `status features` covers Git, Memory, Office, Code Tidy, Local
+Provider and Web Search plus Browser/Computer bridge activity; voice status and
+the Browser Use / Computer Use installed and enabled markers are read with
+`status desktop`.
 
 - Git, Memory, Office, and Local Provider are install-first capabilities.
 - Git and Office installation run on the Desktop when this conversation is

package/src/defaults/skills/setup/references/surfaces.md

@@ -37,9 +37,9 @@ An attached Desktop or TUI may navigate and return `opened:true`.
 - Settings → Providers: API-key, OAuth, local providers, and usage sign-in.
 - Extensions → Plugin → Git & GitHub: Git/GitHub CLI installation and connection.
 - Settings → Connection: web-app pairing and linked devices.
-- Settings → System: update, keep-awake, and Doctor.
-- Projects: Project registration, name, Instructions, Common Instructions, and
-  Core Memories.
+- Settings → System: update, keep-awake, run in background after the window
+  closes, and Doctor.
+- Projects: Project registration, name, Project Memories, and Common Memory.
 - Workflows: workflow packs, Main and Web Search defaults, and agent editing.
 - Extensions → Plugin: Built-in cards and plugins.
 - Extensions → Skill: skills and MCP servers.
@@ -49,12 +49,15 @@ the user to Desktop.
 
 ## Desktop-backed settings
 
-Setup can read and change Desktop appearance, keep-awake, usage pin,
-Computer observe-only, Browser/Computer/voice installation and toggles,
-Projects, Instructions, and linked-device revocation through the attached
+Setup can read and change Desktop appearance, keep-awake, run in background,
+usage pin, Computer observe-only, Browser/Computer/voice installation and
+toggles, Projects, and linked-device revocation through the attached
 Desktop. A receipt identifies `scope:desktop-host`; appearance is not applied
 to the paired browser. No Desktop claimant means no confirmed change.
 
+Computer observe-only has no Desktop settings control; setup is its only
+supported route. Usage pin is the pin toggle on the activity rail usage card.
+
 Schedules/webhooks and workflow/agent/skill definitions use their runtime
 actions directly. These do not require clicking their Desktop rails.
 

package/src/rules/shared/70-delivery.md

@@ -7,6 +7,9 @@
   absolute path, optionally `:line[:column]` (`deliverables/report.docx`,
   `src/app.ts:42`); never a bare name, a path relative to another folder, or a
   `file://` URI.
+- Deliver requested visual artifacts (SVG, diagrams, HTML pages) as saved files
+  and give their path; never paste their source as the answer unless the user
+  asks for the code.
 
 <!-- tools: git -->
 - A commit request includes selecting and staging its changes; a stage-only

package/src/runtime/agent/orchestrator/agent-trace-format.mjs

@@ -410,6 +410,11 @@ function classifyToolFailure(resultText, toolName) {
     if (/\[signal:\s*[^\]]+/i.test(leading)) return 'process/signal';
     return 'command-exit';
   }
+  // edit quotes the file around a miss (the nearest line and a current-file
+  // excerpt). That quoted text is file content, so a word in it such as
+  // "unreadable", "timeout" or "permission" must not pick the category.
+  if (toolName === 'edit' && /^edit failed \(old_string (?:not found|found \d+ times)\b/i.test(leading))
+    return 'runtime/failure';
   if (/compacted-history placeholder/.test(text)) return 'expected-preflight';
   if (/\[tool-input-validation\]/.test(text)) return 'schema/args';
   // These are emitted validation/cancellation contracts, not keywords found

package/src/runtime/agent/orchestrator/config.mjs

@@ -100,7 +100,9 @@ export function buildDefaultConfig(options = {}) {
   providers['mixdog-local'] = { enabled: false };
   return {
     providers,
-    disabledAgents: [...DEFAULT_DISABLED_AGENT_IDS],
+    // The Maintainer also starts off: background upkeep spends model calls, so
+    // it runs only once the user turns it on and picks its model.
+    disabledAgents: [...DEFAULT_DISABLED_AGENT_IDS, 'maintainer'],
     workflow: { active: 'default' },
     orchestrationMode: 'none',
   };
@@ -272,6 +274,11 @@ export function loadConfig(options = {}) {
     recap: { enabled: true },
     developer: {},
     modules: {},
+    // No stored section at all is a brand-new profile: its built-ins start
+    // uninstalled. The defaults above carry presets/recap/modules, which
+    // would otherwise read as a pre-section profile and be grandfathered.
+    // A stored section that failed to parse proves nothing and keeps that path.
+    ...(hasKeys(sectionRaw) ? {} : { builtins: {} }),
   };
 }
 /** In-lock patch of `skills.disabled` only (avoids whole-config lost-update). */

package/src/runtime/agent/orchestrator/context/role-instructions.mjs

@@ -281,7 +281,6 @@ export function composeSystemPrompt(opts) {
   // pre-tool preamble toward English.
   const environmentParts = [
     opts.sessionStartContext,
-    opts.projectInstructionsContext,
     opts.environmentContext,
     opts.languageContext,
   ].map(trimmedPromptSlice);

package/src/runtime/agent/orchestrator/providers/registry-errors.mjs

@@ -0,0 +1,9 @@
+// Error code for a provider init that has no enabled provider to register.
+// The registry refuses such an init to protect its live instances; readers
+// that legitimately run before any provider exists (the model catalog on a
+// fresh install) treat it as "nothing to load" instead of a failure.
+export const NO_ENABLED_PROVIDERS = 'PROVIDERS_NONE_ENABLED';
+
+export function noEnabledProvidersError(message) {
+  return Object.assign(new Error(message), { code: NO_ENABLED_PROVIDERS });
+}

package/src/runtime/agent/orchestrator/providers/registry.mjs

@@ -4,6 +4,7 @@ import { refreshCatalog as refreshMetadataCatalog } from './model-catalog.mjs';
 import { wrapProviderAdmission } from './admission-scheduler.mjs';
 import { createAccountPoolProvider } from './account-pool.mjs';
 import { isInclusiveProvider } from '../../../shared/llm/cost.mjs';
+import { noEnabledProvidersError } from './registry-errors.mjs';
 // OpenAI-compat provider names are self-declared by openai-compat-presets.mjs via
 // OPENAI_COMPAT_PRESETS. No parallel list maintained here.
 const providers = new Map();
@@ -223,7 +224,7 @@ async function _initProvidersUnsynchronized(config, signal = null) {
   // here preserves whatever was already registered.
   const entries = Object.entries(config || {});
   if (entries.length === 0) {
-    throw new Error('[provider] initProviders called with empty config — refusing to clear registry');
+    throw noEnabledProvidersError('[provider] initProviders called with empty config — refusing to clear registry');
   }
   const next = new Map();
   const nextSignatures = new Map();
@@ -258,7 +259,7 @@ async function _initProvidersUnsynchronized(config, signal = null) {
   // Second guard: every entry was disabled. Same reasoning — keep the
   // existing registry rather than going dark.
   if (next.size === 0) {
-    throw new Error('[provider] all providers disabled in config — refusing to clear registry');
+    throw noEnabledProvidersError('[provider] all providers disabled in config — refusing to clear registry');
   }
   // OAuth preservation guard. anthropic-oauth / openai-oauth are NOT stored
   // in mixdog-config.json — buildDefaultConfig injects them at runtime by

package/src/runtime/agent/orchestrator/runtime-core/goal-tasks.mjs

@@ -6,11 +6,13 @@ import { clean } from '../../../shared/clean.mjs';
 // dropped on normalize rather than rejected.
 const TASK_ENTRY_FIELDS = ['id', 'text', 'status', 'kind'];
 
-// Dropped rows remain in the record but are no longer requested work.
+// Dropped rows remain in the record but are no longer requested work. Every
+// row, completed and dropped included, still fills one of the capped slots.
 export function goalTaskProgress(tasks) {
   return {
     tasksCompleted: tasks.filter((task) => task?.status === 'completed').length,
     tasksTotal: tasks.filter((task) => task?.status !== 'dropped').length,
+    taskSlotsUsed: tasks.length,
   };
 }
 
@@ -89,12 +91,18 @@ function taskInputRetains(entry, task) {
 }
 
 export function patchGoalTasks(previous, { updates, tasks } = {}) {
-  const patches = updates ?? [];
-  const additions = tasks ?? [];
-  if (!Array.isArray(patches) || !Array.isArray(additions)) throw new Error('goal updates and tasks must be arrays');
+  const requested = updates ?? [];
+  const entries = tasks ?? [];
+  if (!Array.isArray(requested) || !Array.isArray(entries)) throw new Error('goal updates and tasks must be arrays');
+  const byId = new Map(previous.map((task) => [task.id, { ...task }]));
+  // A new-task entry naming an id this Goal already has can only mean that
+  // task, so it is applied as the task's update. An id the Goal does not have
+  // is still refused below.
+  const addressesExisting = (entry) => byId.has(clean(entry?.id));
+  const patches = [...requested, ...entries.filter(addressesExisting)];
+  const additions = entries.filter((entry) => !addressesExisting(entry));
   if (!patches.length && !additions.length) throw new Error('goal update_tasks requires updates or new tasks');
   if (patches.length > MAX_GOAL_TASKS) throw new Error(`goal updates support at most ${MAX_GOAL_TASKS} entries`);
-  const byId = new Map(previous.map((task) => [task.id, { ...task }]));
   const seen = new Set();
   for (const patch of patches) {
     const id = clean(patch?.id);

package/src/runtime/agent/orchestrator/runtime-core/goal-text.mjs

@@ -3,6 +3,7 @@
 // No filesystem, no runtime coupling — values in, text out.
 
 import { goalTaskProgress } from './goal-tasks.mjs';
+import { MAX_GOAL_TASKS } from './goal-tool-defs.mjs';
 
 function escapeGoalPromptText(value) {
   return String(value ?? '')
@@ -214,7 +215,7 @@ export function goalStateReminder(goal, { reason = '' } = {}) {
   }
   if (reason === 'deadline-reached' && goal.status === 'active') return '';
   const tasks = Array.isArray(goal.tasks) ? goal.tasks : [];
-  const { tasksCompleted, tasksTotal } = goalTaskProgress(tasks);
+  const { tasksCompleted, tasksTotal, taskSlotsUsed } = goalTaskProgress(tasks);
   // Event-specific steering: what the model could not have learned from its own
   // tool results. Standing rules stay in the cached tool description.
   let lead = 'Current durable Goal snapshot:';
@@ -233,7 +234,7 @@ export function goalStateReminder(goal, { reason = '' } = {}) {
     ...(goal.status === 'blocked' ? [BLOCKED_LINE] : []),
     '',
     `Objective: ${escapeGoalPromptText(goal.objective)}`,
-    `Status: ${escapeGoalPromptText(goal.status)} · tasks ${tasksCompleted}/${tasksTotal}`,
+    `Status: ${escapeGoalPromptText(goal.status)} · tasks ${tasksCompleted}/${tasksTotal} · task slots used ${taskSlotsUsed}/${MAX_GOAL_TASKS}`,
     ...(goal.blocker ? [`Waiting or stop reason: ${escapeGoalPromptText(goal.blocker)}`] : []),
     ...(goal.revision ? [`Revision: ${goal.revision}`] : []),
     ...goalTimeLines(goal),

package/src/runtime/agent/orchestrator/runtime-core/goal-tool-defs.mjs

@@ -16,7 +16,7 @@ const taskFields = {
     type: 'string',
     minLength: 1,
     maxLength: MAX_GOAL_TASK_TEXT_LENGTH,
-    description: 'Required work or verification outcome.',
+    description: 'Brief work/check; results go in reply.',
   },
   status: {
     type: 'string',

package/src/runtime/agent/orchestrator/runtime-core/goal-tool-exec.mjs

@@ -22,6 +22,7 @@ function toolReply(ctx, id, goal, { full = false, previousIds = null } = {}) {
       status: goal.status,
       tasksCompleted: goal.tasksCompleted,
       tasksTotal: goal.tasksTotal,
+      taskSlotsUsed: goal.taskSlotsUsed,
       tasksUpdatedAt: goal.tasksUpdatedAt,
       timeUsedMs: goal.timeUsedMs,
     };

package/src/runtime/agent/orchestrator/session/manager/session-prompt-composition.mjs

@@ -86,7 +86,7 @@ export function composeSessionSystem(opts, { profile, providerName, modelName, s
   const languageContext = leadOnly ? _buildLeadLanguageContext() : '';
   const shellEnvironmentContext = buildShellEnvironmentContext(opts, ownerIsAgent, surface.toolsForRouting);
   // Persisted env tail: refreshSessionBp3Environment rebuilds the env block
-  // as [session, project, bp3EnvironmentContext], so the language block must
+  // as [session, bp3EnvironmentContext], so the language block must
   // already sit at the end of this string to stay last after a refresh.
   const environmentTailContext = [shellEnvironmentContext, languageContext].filter(Boolean).join('\n\n---\n\n');
   const composed = composeSystemPrompt({

package/src/runtime/agent/orchestrator/tools/builtin/arg-guard.mjs

@@ -174,6 +174,23 @@ function hasMultipleAbsoluteWindowsPaths(value) {
   return Array.isArray(matches) && matches.length > 1;
 }
 
+// A string that only lists absolute Windows paths ("C:\a C:\b", "C:\a,C:\b",
+// "[C:/a, C:/b]", '["C:/a", "D:/b"]') splits exactly: every piece starts at a
+// drive root, and no drive root can occur inside a Windows path, so spaces
+// within a path stay put. Any other text around the paths returns null.
+function splitListedAbsoluteWindowsPaths(value) {
+  const body = value
+    .trim()
+    .replace(/^\[([\s\S]*)\]$/, '$1')
+    .replace(/^[\s,;]+|[\s,;]+$/g, '');
+  const pieces = body
+    .split(/[\s,;]+(?=["']?[A-Za-z]:[\\/])/)
+    .map((piece) => piece.replace(/^(["'])(.*)\1$/, '$2'));
+  return pieces.every((piece) => /^[A-Za-z]:[\\/]/.test(piece) && !/[A-Za-z]:[\\/]/.test(piece.slice(3)))
+    ? pieces
+    : null;
+}
+
 function isFiniteInt(v) {
   return typeof v === 'number' && Number.isFinite(v) && Math.floor(v) === v;
 }
@@ -418,8 +435,17 @@ function guardGrep(a) {
       return `Error: grep arg "${k}" must be string (got ${describeType(a[k])})`;
     }
   }
-  // Independent explicit scopes share one request; no inferred path splitting.
+  // Independent explicit scopes share one request. A string that only lists
+  // absolute paths is those scopes; any other string holding several drive
+  // roots is refused rather than guessed at.
   for (const k of ['path', 'root']) {
+    if (hasOwn(a, k) && hasMultipleAbsoluteWindowsPaths(a[k])) {
+      const listed = splitListedAbsoluteWindowsPaths(a[k]);
+      if (!listed) {
+        return `Error: grep arg "${k}" contains multiple absolute paths in one string. Use one common parent path plus glob, or separate grep calls.`;
+      }
+      a[k] = listed;
+    }
     if (hasOwn(a, k) && Array.isArray(a[k])) {
       if (a[k].length === 0 || a[k].length > PUBLIC_PATH_BATCH_LIMIT || !a[k].every(isNonEmptyString)) {
         return `Error: grep arg "${k}" must contain 1-${PUBLIC_PATH_BATCH_LIMIT} non-empty path strings`;
@@ -429,9 +455,6 @@ function guardGrep(a) {
     if (hasOwn(a, k) && !isString(a[k])) {
       return `Error: grep arg "${k}" must be string or string[] (got ${describeType(a[k])})`;
     }
-    if (hasOwn(a, k) && hasMultipleAbsoluteWindowsPaths(a[k])) {
-      return `Error: grep arg "${k}" contains multiple absolute paths in one string. Use one common parent path plus glob, or separate grep calls.`;
-    }
   }
   for (const k of ['head_limit', 'offset']) {
     const err = checkIntInRange(a, k, 0, MAX_INT);

package/src/runtime/agent/orchestrator/tools/builtin/read-batch.mjs

@@ -33,7 +33,9 @@ export function sliceReadBodyByLines(body, origOffset, origLimit, readOffsetBase
       if (ln < minSeen) minSeen = ln;
       if (ln > maxSeen) maxSeen = ln;
       if (ln >= firstLine && ln <= lastLine) kept.push(line);
-    } else if (kept.length === 0 && footerIdx === -1) {
+    } else if (kept.length === 0 && footerIdx === -1 && !Number.isFinite(maxSeen)) {
+      // Only a preamble before the first numbered row; a blank line or a
+      // truncation marker after the rows is not this slot's content.
       kept.push(line);
     }
   }

package/src/runtime/agent/orchestrator/tools/builtin/read-tool/batch-dispatch.mjs

@@ -42,7 +42,8 @@ async function estimateTaskBytes(entry, workDir) {
   if (!st?.isFile()) return Infinity;
   const lines = Math.max(1, st.size / AVG_LINE_BYTES);
   let need = st.size + st.size / MIN_LINE_BYTES * LINE_PREFIX_BYTES;
-  const limit = Number(entry?.limit);
+  // A coalesced entry reads its whole union window, not only its own slot.
+  const limit = Number(readEntryCoalescedDiskWindow(entry)?.limit ?? entry?.limit);
   if (Number.isFinite(limit) && limit > 0) need *= Math.min(1, limit / lines);
   return Math.ceil(need) + READ_RENDER_SLACK_BYTES;
 }

package/src/runtime/agent/orchestrator/tools/code-graph/build.mjs

@@ -100,9 +100,12 @@ function _throwIfAborted(signal) {
   if (signal?.aborted) throw new Error('aborted');
 }
 
-function codeGraphBuildInvalidatedError() {
+// `graph` is the build that finished anyway: the tree as of its own manifest,
+// never cached as current. The last retry answers from it instead of failing.
+function codeGraphBuildInvalidatedError(graph = null) {
   const error = new Error('code-graph build invalidated during prewarm');
   error.code = 'ERR_CODE_GRAPH_BUILD_INVALIDATED';
+  if (graph) error.graph = graph;
   return error;
 }
 
@@ -115,7 +118,12 @@ export async function _retryCodeGraphBuildAfterInvalidation(run, { signal = null
     try {
       return await run(attempt);
     } catch (error) {
-      if (signal?.aborted || !isCodeGraphBuildInvalidatedError(error) || attempt === 1) {
+      if (signal?.aborted || !isCodeGraphBuildInvalidatedError(error)) throw error;
+      // Files kept changing through the retry too (another session editing
+      // the same tree). The finished graph is a consistent snapshot a few
+      // seconds old; answer this query from it rather than fail it.
+      if (attempt === 1) {
+        if (error.graph) return error.graph;
         throw error;
       }
     }
@@ -159,7 +167,7 @@ async function _validateDiskCodeGraphHit({
   if (diskEntry.signature !== signature) return { graph: null, manifest, signature };
   const graph = deserializeGraph(graphCwd, diskEntry);
   if (!graph) return { graph: null, manifest, signature };
-  if (getGeneration(graphCwd) !== genAtStart) return { invalidated: true };
+  if (getGeneration(graphCwd) !== genAtStart) return { invalidated: true, graph };
   setMemoryCache(graphCwd, { ts: now, signature, graph });
   return { graph, manifest, signature };
 }
@@ -195,7 +203,7 @@ export async function _runDiskCodeGraphFastPath({
     _throwIfAborted(signal);
     const hit = await validateDiskHit({ graphCwd, diskEntry, genAtStart, signal });
     _throwIfAborted(signal);
-    if (hit?.invalidated) throw codeGraphBuildInvalidatedError();
+    if (hit?.invalidated) throw codeGraphBuildInvalidatedError(hit.graph);
     if (hit?.graph) return hit.graph;
     _throwIfAborted(signal);
     const workerPromise = spawnWorker(release, hit?.manifest || null, hit?.signature || null);
@@ -463,7 +471,7 @@ export function _spawnCodeGraphWorker(
               // manifest lock.
               setDiskCache(graphCwd, msg.graph, { persist: false });
             }
-            settle(genStillCurrent ? msg.graph : codeGraphBuildInvalidatedError());
+            settle(genStillCurrent ? msg.graph : codeGraphBuildInvalidatedError(msg.graph));
           } else {
             settle(_codeGraphWorkerFailure(msg));
           }

package/src/runtime/computer-bridge/error-recovery.mjs

@@ -79,7 +79,7 @@ function recoveryForCode(code, args) {
       code,
       next: 'wait_for_user',
       guidance:
-        'Computer Use yielded to the user. Call wait_for_user for bounded waiting. Ordinary physical input may resume after the host-configured quiet interval (default 5 seconds); explicit stops and uncertain cleanup/observation require the user. Timeout does not authorize input. After resumed, capture fresh state; never replay interrupted input. Manual Resume is also available on the overlay.',
+        "Computer Use yielded to the user. Call wait_for_user for bounded waiting. The user's Resume on the overlay continues the pause, and ordinary physical input may also resume after the host-configured quiet interval (default 5 seconds); explicit stops and uncertain cleanup/observation require the user. Stop cancels the task. Timeout does not authorize input. After resumed, capture fresh state; never replay interrupted input.",
     };
   }
   if (DIAGNOSE_CODES.has(code)) {

package/src/runtime/shared/config-patch.mjs

@@ -25,6 +25,8 @@ function applyField(current, path, change) {
   const next = isPlainObject(current) ? { ...current } : {};
   const [key, ...rest] = path;
   if (change.remove && rest.length && !Object.hasOwn(next, key)) return next;
+  // Seed-only field: written where it is missing, never over a stored value.
+  if (change.ifAbsent && !rest.length && Object.hasOwn(next, key)) return next;
   if (!rest.length && change.remove) {
     delete next[key];
   } else {

package/src/runtime/shared/user-data-guard.mjs

@@ -28,7 +28,7 @@ function getBackupRoot() {
   return process.env.MIXDOG_USER_DATA_BACKUP_ROOT || join(mixdogConfigBaseDir(), 'backups', 'user-data');
 }
 
-const USER_DATA_FILES = ['mixdog-config.json', 'instructions.md', 'user-workflow.md'];
+const USER_DATA_FILES = ['mixdog-config.json'];
 
 const USER_DATA_DIRS = ['schedules', 'webhooks', 'workflows'];
 

package/src/session-runtime/config-lifecycle.mjs

@@ -102,10 +102,20 @@ export function createConfigLifecycle({
     const adopted = adoptConfig(nextConfig, { hasSecrets });
     const changes = cfgMod.createConfigPatch(configSaveBaseline, adopted);
     configSaveBaseline = structuredClone(adopted);
-    if (changes.length) writers.queueConfigChanges(changes);
+    if (changes.length) writers.queueConfigChanges([...changes, ...seedChanges(adopted, changes)]);
     return adopted;
   }
 
+  // A fresh profile's install markers (an empty `builtins`) and off-by-default
+  // agents equal the defaults, so no diff ever carries them — yet on disk
+  // their absence reads as a grandfathered profile with every agent on. The
+  // first write seeds them where the stored section lacks them.
+  function seedChanges(config, changes) {
+    return ['builtins', 'disabledAgents']
+      .filter((key) => config[key] !== undefined && !changes.some((change) => change.path[0] === key))
+      .map((key) => ({ path: [key], value: structuredClone(config[key]), ifAbsent: true }));
+  }
+
   function scheduleSkillsSave(names) {
     // This field belongs to its dedicated writer, not a later unrelated save.
     configSaveBaseline.skills = structuredClone(getConfig().skills);

package/src/session-runtime/cwd-plugins/core-memory-context.mjs

@@ -24,7 +24,7 @@ export function createCoreMemoryContext({ getCurrentCwd, getConfig, bootProfile,
   async function loadCoreMemoryContext() {
     // User-curated core memory injects into new sessions by default. The
     // Memory toggle (settings → General) OFF skips ONLY this accumulated
-    // core-memory block — profile and Project Instructions inject regardless.
+    // core-memory block — the profile injects regardless.
     if (!(featureEnvOverride('MIXDOG_FEATURE_MEMORY') ?? memoryToolsEnabled(getConfig(), true))) {
       bootProfile('core-memory:disabled');
       return '';

package/src/session-runtime/cwd-plugins/plugin-status.mjs

@@ -1,6 +1,7 @@
 // cwd-plugins/plugin-status.mjs — the registered-plugin status list with its
 // per-root caches (manifest keyed on mtime, MCP discovery and skill-file count
 // on a short TTL).
+import { readFileSync } from 'node:fs';
 import { discoverPluginMcp } from '../../runtime/agent/orchestrator/runtime-core/plugin-mcp.mjs';
 import { pluginMetadata } from '../../runtime/shared/plugin-metadata.mjs';
 
@@ -35,11 +36,25 @@ export function createPluginStatus({
     }
     return key;
   }
+  // A manifest file that exists but is not a JSON object is breakage.
+  function manifestInvalid(root) {
+    for (const rel of ['.codex-plugin/plugin.json', 'plugin.json']) {
+      const file = resolve(root, rel);
+      if (!existsSync(file)) continue;
+      try {
+        const parsed = JSON.parse(readFileSync(file, 'utf8'));
+        if (!parsed || typeof parsed !== 'object' || Array.isArray(parsed)) return true;
+      } catch {
+        return true;
+      }
+    }
+    return false;
+  }
   function cachedPluginData(root) {
     const key = manifestMtimeKey(root);
     const hit = pluginRootCache.get(root);
     if (hit && hit.key === key) return hit;
-    const entry = { key, manifest: pluginManifest(root) };
+    const entry = { key, manifest: pluginManifest(root), invalid: manifestInvalid(root) };
     pluginRootCache.set(root, entry);
     return entry;
   }
@@ -65,8 +80,9 @@ export function createPluginStatus({
 
   function registeredPlugin(entry, configuredMcp) {
     const root = clean(entry.root);
-    if (!root || !existsSync(root)) return null;
-    const manifest = cachedPluginData(root).manifest;
+    if (!root) return null;
+    if (!existsSync(root)) return { missing: true, id: clean(entry.id) || clean(entry.name) || root, name: clean(entry.name) || clean(entry.id) || root.split(/[\\/]/).pop() || root };
+    const { manifest, invalid } = cachedPluginData(root);
     const name = clean(manifest.name) || clean(manifest.id) || clean(entry.name) || root.split(/[\\/]/).pop() || root;
     const { mcpScript, mcpInline } = cachedMcpDiscovery(root);
     const plugin = {
@@ -89,6 +105,7 @@ export function createPluginStatus({
       mcpScript,
       mcpInline,
     };
+    if (invalid) plugin.invalid = true;
     plugin.mcpServerName = pluginMcpServerName(plugin);
     plugin.mcpEnabled =
       Object.hasOwn(configuredMcp, plugin.mcpServerName) ||
@@ -101,9 +118,11 @@ export function createPluginStatus({
     const dataDir = cfgMod.getPluginData?.();
     const configuredMcp = config?.mcpServers && typeof config.mcpServers === 'object' ? config.mcpServers : {};
     const plugins = [];
+    const missing = [];
     for (const entry of listRegisteredPlugins({ dataDir })) {
       const plugin = registeredPlugin(entry, configuredMcp);
-      if (plugin) plugins.push(plugin);
+      if (plugin?.missing) missing.push({ id: plugin.id, name: plugin.name, enabled: entry.enabled !== false });
+      else if (plugin) plugins.push(plugin);
     }
     plugins.sort((a, b) => {
       if (a.source !== b.source) return a.source.localeCompare(b.source);
@@ -113,6 +132,7 @@ export function createPluginStatus({
     return {
       count: plugins.length,
       plugins,
+      missing,
       roots: {
         registry: admin.registryPath,
         installed: admin.installRoot,