@delorenj/pjangler 1.5.53 → 1.5.54

package/dist/index.js

@@ -457,9 +457,44 @@ var init_notebookSettingsValidation = __esm({
 });
 
 // src/project/executionBinding.ts
+function executionReadiness(manifest) {
+  const execution = manifest.execution;
+  if (!execution || execution.mode === "legacy") return [];
+  const errors = [];
+  if (!["shadow", "managed"].includes(execution.mode)) errors.push("execution.mode must be legacy, shadow or managed");
+  if (!manifest.project_id) errors.push("canonical project_id missing");
+  if (manifest.ticket_provider?.type !== "plane" || !manifest.ticket_provider.workspace || !manifest.ticket_provider.board_id) errors.push("exact Plane binding missing");
+  if (execution.policy_version !== 2 || !execution.skill_version) errors.push("execution policy or skill pin missing");
+  for (const lane of EXECUTION_LANES) if (!execution.states?.[lane]) errors.push(`lane binding missing: ${lane}`);
+  for (const pin of ["pilot_bundle_sha256", "momo_bundle_sha256"]) if (!/^[a-f0-9]{64}$/.test(execution[pin] ?? "")) errors.push(`${pin} missing`);
+  if (!execution.working_label) errors.push("working label binding missing");
+  if (!execution.actors?.[execution.pm_actor] || execution.actors[execution.pm_actor].role !== "pm") errors.push("PM actor enrollment missing");
+  if (!execution.actors?.[execution.controller_actor] || execution.actors[execution.controller_actor].role !== "operator") errors.push("controller repair actor enrollment missing");
+  const ids = /* @__PURE__ */ new Set();
+  for (const [name, actor] of Object.entries(execution.actors ?? {})) {
+    if (!actor.native_user_id || !actor.key_ref?.startsWith("op://") || !actor.runtime_id) errors.push(`actor ${name}: native identity, op reference and runtime required`);
+    if (ids.has(actor.native_user_id)) errors.push(`actor ${name}: duplicate native identity`);
+    ids.add(actor.native_user_id);
+    if (!["pm", "operator", "reviewer", "interactive"].includes(actor.role)) errors.push(`actor ${name}: invalid role`);
+    if (name === execution.pm_actor && (!Array.isArray(actor.runtime?.planner_argv) || !actor.runtime.planner_argv.length || actor.runtime.planner_argv.some((x) => typeof x !== "string" || !x || x.includes("\0")))) errors.push("PM planner argv missing");
+    if (actor.runtime?.adapter !== "systemd" || !/^[a-zA-Z0-9_-]+$/.test(actor.runtime?.unit_prefix ?? "")) errors.push(`actor ${name}: supervised runtime missing`);
+  }
+  if (execution.legacy_writers_fenced !== true) errors.push("legacy writers not fenced");
+  return errors;
+}
+function validateExecutionBinding(manifest) {
+  if (!manifest.execution) return;
+  if (typeof manifest.execution !== "object" || Array.isArray(manifest.execution)) throw new Error("execution must be an object");
+  if (manifest.execution.mode === "managed") {
+    const errors = executionReadiness(manifest);
+    if (errors.length) throw new Error(`Managed execution not ready: ${errors.join("; ")}`);
+  } else if (!["legacy", "shadow"].includes(manifest.execution.mode)) throw new Error("invalid execution mode");
+}
+var EXECUTION_LANES;
 var init_executionBinding = __esm({
   "src/project/executionBinding.ts"() {
     "use strict";
+    EXECUTION_LANES = ["Backlog", "Needs Re-evaluation", "Todo", "In Progress", "E2E Testing & QA", "Ready for Documentation", "Done", "Needs Attention", "Cancelled"];
   }
 });
 
@@ -472,6 +507,46 @@ function normalizeProjectId2(value) {
     throw new RegistryError(error instanceof Error ? error.message : String(error));
   }
 }
+function object(value) {
+  return !!value && typeof value === "object" && !Array.isArray(value);
+}
+function validateManifestShape(manifest, path) {
+  validateExecutionBinding(manifest);
+  const fail2 = (field2, shape) => {
+    throw new RegistryError(`Manifest ${path}: ${field2} must be ${shape}`);
+  };
+  const strings = (value, names, prefix = "") => {
+    for (const name of names) if (value[name] !== void 0 && typeof value[name] !== "string") fail2(`${prefix}${name}`, "a string");
+  };
+  strings(manifest, ["project_name", "name", "project_description", "description", "status", "repo_path", "created_at", "updated_at"]);
+  for (const field2 of ["ticket_provider", "agents", "template", "notebook", "automation"]) if (manifest[field2] !== void 0 && !object(manifest[field2])) fail2(field2, "an object");
+  if (manifest.source_artifacts !== void 0 && !Array.isArray(manifest.source_artifacts)) fail2("source_artifacts", "an array");
+  for (const [index, artifact] of (manifest.source_artifacts ?? []).entries()) {
+    if (!object(artifact)) fail2(`source_artifacts.${index}`, "an object");
+    strings(artifact, ["kind", "path", "package_name"], `source_artifacts.${index}.`);
+  }
+  if (manifest.ticket_provider) strings(manifest.ticket_provider, ["type", "workspace", "identifier", "identifier_source", "identifier_fetched_at", "board_id", "board_confirmed_at", "board_url", "state", "scope_label"], "ticket_provider.");
+  if (manifest.ticket_provider?.scope_default !== void 0 && typeof manifest.ticket_provider.scope_default !== "boolean") fail2("ticket_provider.scope_default", "a boolean");
+  for (const [name, agent] of Object.entries(manifest.agents ?? {})) {
+    if (!object(agent)) fail2(`agents.${name}`, "an object");
+    strings(agent, ["role", "role_dir", "provisioning_state"], `agents.${name}.`);
+  }
+  if (manifest.template?.commonproject !== void 0) {
+    if (!object(manifest.template.commonproject)) fail2("template.commonproject", "an object");
+    const template = manifest.template.commonproject;
+    if (template.enabled !== void 0 && typeof template.enabled !== "boolean") fail2("template.commonproject.enabled", "boolean");
+    strings(template, ["primary_language", "project_type"], "template.commonproject.");
+  }
+  for (const field2 of ["binding", "policy"]) if (manifest.notebook?.[field2] !== void 0 && !object(manifest.notebook[field2])) fail2(`notebook.${field2}`, "an object");
+  if (manifest.notebook?.binding) strings(manifest.notebook.binding, ["provider", "state", "notebook_name", "blocked_reason", "notebook_id", "overview_note_id", "created_at", "updated_at"], "notebook.binding.");
+  if (manifest.notebook?.policy) {
+    try {
+      validateGlobalNotebookConfig({ defaults: manifest.notebook.policy });
+    } catch (error) {
+      throw new RegistryError(`Manifest ${path}: invalid notebook policy: ${String(error)}`);
+    }
+  }
+}
 function recordFromManifest(manifest, path) {
   const id = normalizeProjectId2(manifest.project_id ?? manifest.project_slug);
   const { project_slug: _old, project_name: _name, project_description: _description, notebook, ...rest } = manifest;
@@ -1641,12 +1716,40 @@ function resolveSourceSkillPath(sourceSkill, env2 = process.env) {
   const hint = `${searched} Add project-specific roots with ${PROJECT_SOURCE_SKILL_ROOTS_ENV}.`;
   throw new Error(`Source skill not found: ${sourceSkill}.${hint}`);
 }
+function looksLikePath(value) {
+  return /^(?:\/|~\/|\.{1,2}\/)/.test(value);
+}
+function normalizeLegacyManifest(manifest) {
+  const artifacts = manifest.source_artifacts;
+  if (!Array.isArray(artifacts)) return { manifest, notes: [] };
+  const notes = [];
+  const normalized = artifacts.map((artifact, index) => {
+    if (typeof artifact !== "string" || !looksLikePath(artifact)) return artifact;
+    notes.push(`.project.json source_artifacts.${index}: bare path normalized to {"kind": "${LEGACY_SOURCE_ARTIFACT_KIND}", "path": "${artifact}"}`);
+    return { kind: LEGACY_SOURCE_ARTIFACT_KIND, path: artifact };
+  });
+  return notes.length ? { manifest: { ...manifest, source_artifacts: normalized }, notes } : { manifest, notes };
+}
 function planProjectInit(input) {
   if (!input.name.trim()) throw new Error("Project name is required");
   const targetDir = resolve11(input.targetDir ?? defaultProjectTargetDir(input.name, input.cwd));
   const localManifestPath = join18(targetDir, ".project.json");
   const localManifestContent = existsSync11(localManifestPath) ? readFileSync17(localManifestPath, "utf8") : void 0;
-  const localManifest = localManifestContent === void 0 ? void 0 : JSON.parse(localManifestContent);
+  let localManifest;
+  const manifestNotes = [];
+  if (localManifestContent !== void 0) {
+    let parsed;
+    try {
+      parsed = JSON.parse(localManifestContent);
+    } catch {
+      throw new Error(`Malformed JSON: ${localManifestPath}`);
+    }
+    if (!parsed || typeof parsed !== "object" || Array.isArray(parsed)) throw new Error(`Expected a JSON object: ${localManifestPath}`);
+    const normalized = normalizeLegacyManifest(parsed);
+    localManifest = normalized.manifest;
+    manifestNotes.push(...normalized.notes);
+    validateManifestShape(localManifest, localManifestPath);
+  }
   const localId = localManifest?.project_id ?? localManifest?.project_slug;
   const slug = normalizeProjectId(input.projectSlug ?? localId ?? slugifyProjectName(input.name));
   if (localId && normalizeProjectId(localId) !== slug) throw new Error(`Project ID ${slug} conflicts with authoritative manifest ${localId}`);
@@ -1741,6 +1844,7 @@ function planProjectInit(input) {
   validateNoDuplicateProject(registry, project, overwrite);
   const pjanglerRoot = resolve11(input.pjanglerRoot ?? resolvePjanglerRoot());
   const manifest = projectManifestFromRegistryProject(project);
+  validateManifestShape(manifest, localManifestPath);
   const apply = input.apply ?? false;
   const live = input.live ?? false;
   const provisionTicketBoard = input.provisionTicketBoard ?? true;
@@ -1796,7 +1900,7 @@ function planProjectInit(input) {
     project,
     manifest,
     actions,
-    ...input.boardUrl !== void 0 ? { warnings: [BOARD_URL_DEPRECATION_WARNING] } : {}
+    ...input.boardUrl !== void 0 || manifestNotes.length ? { warnings: [...input.boardUrl !== void 0 ? [BOARD_URL_DEPRECATION_WARNING] : [], ...manifestNotes] } : {}
   };
 }
 function linkTicketProviderBoard(plan, action, boardId, identifier, now = /* @__PURE__ */ new Date()) {
@@ -2264,7 +2368,7 @@ function expandHome(path) {
 function isRecord3(value) {
   return typeof value === "object" && value !== null && !Array.isArray(value);
 }
-var PROJECT_SOURCE_SKILL_ROOTS_ENV, TICKET_PROVIDER_ADAPTERS_ENV, PROJECT_REGISTRY_SCHEMA_VERSION, DEFAULT_NEW_PROJECT_STATUS, PROJECT_TYPES, PROJECT_TYPE_LANGUAGES, PROJECT_TYPE_SENTINELS, BOARD_URL_DEPRECATION_WARNING, PROJECT_IDENTIFIER_SOURCES, IDENTIFIER_ASSIGNING_PROVIDERS, TICKET_PROVIDER_STATES, IDENTIFIER_REPAIR_COMMAND, DEFAULT_SOURCE_SKILL_ROOTS, PROJECT_REGISTRY_OWNED_KEYS, PROJECT_NOTEBOOK_OWNED_KEYS, TICKET_PROVIDER_OWNED_KEYS, GLOBAL_NOTEBOOK_OWNED_KEYS, GLOBAL_NOTEBOOK_AUTH_OWNED_KEYS, GLOBAL_NOTEBOOK_DEFAULTS_OWNED_KEYS, GLOBAL_NOTEBOOK_LIMITS_OWNED_KEYS, GLOBAL_NOTEBOOK_SUMMARIZER_OWNED_KEYS, SAFE_PATH_SEGMENT;
+var PROJECT_SOURCE_SKILL_ROOTS_ENV, TICKET_PROVIDER_ADAPTERS_ENV, PROJECT_REGISTRY_SCHEMA_VERSION, DEFAULT_NEW_PROJECT_STATUS, PROJECT_TYPES, PROJECT_TYPE_LANGUAGES, PROJECT_TYPE_SENTINELS, BOARD_URL_DEPRECATION_WARNING, PROJECT_IDENTIFIER_SOURCES, IDENTIFIER_ASSIGNING_PROVIDERS, TICKET_PROVIDER_STATES, IDENTIFIER_REPAIR_COMMAND, DEFAULT_SOURCE_SKILL_ROOTS, PROJECT_REGISTRY_OWNED_KEYS, PROJECT_NOTEBOOK_OWNED_KEYS, TICKET_PROVIDER_OWNED_KEYS, GLOBAL_NOTEBOOK_OWNED_KEYS, GLOBAL_NOTEBOOK_AUTH_OWNED_KEYS, GLOBAL_NOTEBOOK_DEFAULTS_OWNED_KEYS, GLOBAL_NOTEBOOK_LIMITS_OWNED_KEYS, GLOBAL_NOTEBOOK_SUMMARIZER_OWNED_KEYS, SAFE_PATH_SEGMENT, LEGACY_SOURCE_ARTIFACT_KIND;
 var init_project = __esm({
   "src/project/index.ts"() {
     "use strict";
@@ -2320,6 +2424,7 @@ var init_project = __esm({
     GLOBAL_NOTEBOOK_LIMITS_OWNED_KEYS = Object.keys(DEFAULT_NOTEBOOK_LIMITS);
     GLOBAL_NOTEBOOK_SUMMARIZER_OWNED_KEYS = ["executable", "args"];
     SAFE_PATH_SEGMENT = /^[A-Za-z0-9](?:[A-Za-z0-9._-]*[A-Za-z0-9])?$/;
+    LEGACY_SOURCE_ARTIFACT_KIND = "reference";
   }
 });
 
@@ -6353,6 +6458,10 @@ function backupToSnapshot(backup) {
   }
   return snapshot;
 }
+function removeEntry(full, stat) {
+  if (stat.isDirectory() && !stat.isSymbolicLink()) rmSync(full, { recursive: true, force: true });
+  else unlinkSync(full);
+}
 function restoreSingleEntry(root, rel, entry) {
   const full = rel === "." ? root : join3(root, rel);
   let currentStat;
@@ -6363,7 +6472,7 @@ function restoreSingleEntry(root, rel, entry) {
   }
   if (entry.kind === "dir") {
     if (currentStat && (!currentStat.isDirectory() || currentStat.isSymbolicLink())) {
-      rmSync(full, { recursive: true, force: true });
+      removeEntry(full, currentStat);
       currentStat = void 0;
     }
     if (!currentStat) mkdirSync2(full, { recursive: true });
@@ -6374,7 +6483,7 @@ function restoreSingleEntry(root, rel, entry) {
   if (entry.kind === "link") {
     if (currentStat) {
       if (currentStat.isSymbolicLink() && readlinkSync2(full) === entry.target) return;
-      rmSync(full, { recursive: true, force: true });
+      removeEntry(full, currentStat);
     }
     symlinkSync(entry.target, full);
     return;
@@ -6383,7 +6492,7 @@ function restoreSingleEntry(root, rel, entry) {
     if ((currentStat.mode & 4095) === entry.mode && readFileSync2(full).equals(entry.bytes)) return;
     unlinkSync(full);
   } else if (currentStat) {
-    rmSync(full, { recursive: true, force: true });
+    removeEntry(full, currentStat);
   }
   writeFileSync2(full, entry.bytes);
   chmodSync(full, entry.mode);
@@ -6992,10 +7101,10 @@ function openDisplacedStash(projectRoot) {
           index.push({ rel, kind: "link", target });
           count++;
         } else if (bytes) {
-          const object = createHash4("sha256").update(bytes).digest("hex");
-          const objectPath = join5(open(), "objects", object);
+          const object2 = createHash4("sha256").update(bytes).digest("hex");
+          const objectPath = join5(open(), "objects", object2);
           if (!existsSync3(objectPath)) writeFileSync3(objectPath, bytes);
-          index.push({ rel, kind: "file", mode: stat.mode & 4095, object });
+          index.push({ rel, kind: "file", mode: stat.mode & 4095, object: object2 });
           count++;
         } else if (stat.isDirectory()) {
           open();
@@ -9033,9 +9142,13 @@ async function predictRootCollisions(ctx, incoming) {
 async function auditProjectSkills(ctx) {
   const result2 = await inspectStatus(skillCoreOptions(ctx));
   const details = skillDiagnostics(result2.findings);
+  let findings = result2.findings.filter((finding2) => finding2.severity !== "info").length;
   details.push(...(result2.data?.changes ?? []).map((change) => `${change.action}: ${change.path}`));
+  const pendingChanges = (result2.data?.changes ?? []).length;
   const plan = planSkillRoots(ctx.repoRoot);
-  details.push(...skillRootsSummary(plan));
+  const rootLines = skillRootsSummary(plan);
+  details.push(...rootLines);
+  findings += rootLines.length;
   const conflict = activationConflict(ctx, result2.findings);
   let conflictResolvable = false;
   if (conflict?.kind === "alias") conflictResolvable = plan.clean;
@@ -9043,6 +9156,7 @@ async function auditProjectSkills(ctx) {
     const predictions = await predictRootCollisions(ctx, []);
     conflictResolvable = predictions.length > 0 && predictions.every(({ decision }) => decision.action !== "block");
     for (const { decision } of predictions) {
+      if (decision.action === "block") findings += 1;
       details.push(decision.action === "block" ? `blocked: ${decision.detail}` : `resolvable root collision: ${decision.detail.replace(/^replaced/, "replace")}`);
     }
   }
@@ -9051,7 +9165,10 @@ async function auditProjectSkills(ctx) {
   const installerOnly = errors.length > 0 && await installerRefusalsResolvable(ctx, errors, handoff);
   if (installerOnly) details.push("resolvable: every refusal is at a skill the bmad-method installer provides; migrate excludes the inherited selection and releases the replaced links");
   if (handoff.skipped) details.push(`installer skill handoff unavailable: ${handoff.skipped}`);
-  if (handoff.restored.length) details.push(...handoff.restored.map((name) => `stale exclusion: ${name} was excluded for the bmad-method installer's copy, which is gone; migrate restores the inherited catalog skill`));
+  if (handoff.restored.length) {
+    findings += handoff.restored.length;
+    details.push(...handoff.restored.map((name) => `stale exclusion: ${name} was excluded for the bmad-method installer's copy, which is gone; migrate restores the inherited catalog skill`));
+  }
   if (result2.exit === 2 || result2.exit === 3) details.push(migrationGuidance(ctx));
   const changes = result2.data?.changes ?? [];
   const receiptOnly = result2.exit === 6 && changes.length > 0 && changes.every((change) => change.action === "write-receipt") && !result2.findings.some((finding2) => finding2.severity === "error");
@@ -9063,6 +9180,8 @@ async function auditProjectSkills(ctx) {
     status: result2.exit === 0 ? staleHandoff ? "warn" : "pass" : result2.exit === 4 || receiptOnly ? "warn" : "fail",
     summary: result2.exit === 0 ? "Skillex declaration and activation are in parity" : receiptOnly ? "Skillex activation is in parity; its receipt predates the current catalog commit" : `Skillex inspection returned exit ${result2.exit}`,
     details,
+    findings,
+    pendingChanges,
     fixable: result2.exit === 0 || result2.exit === 6 || conflictResolvable || installerOnly || staleHandoff || result2.findings.some((finding2) => finding2.code === "E_NO_PROJECT_MANIFEST")
   };
 }
@@ -12104,28 +12223,54 @@ function consolidatedBmadConfig(repoRoot) {
   if (!existsSync8(path)) return { status: "absent" };
   let parsed;
   try {
-    parsed = YAML4.parse(readText(path));
+    parsed = YAML4.parse(readText(path), { uniqueKeys: false });
   } catch (error) {
-    return { status: "unusable", reason: `could not be parsed: ${error instanceof Error ? error.message.split("\n")[0] : String(error)}` };
+    const reason = error instanceof Error ? error.message.split("\n")[0].replace(/:\s*$/, "") : String(error);
+    return { status: "unusable", reason: `could not be parsed: ${reason}` };
   }
   if (!parsed || typeof parsed !== "object" || Array.isArray(parsed)) {
     return { status: "unusable", reason: "is not a YAML mapping" };
   }
   return { status: "mapping", sections: new Set(Object.keys(parsed)) };
 }
+var BMAD_SCAFFOLD_REMEDY = "pj migrate bmad.scaffold";
+function gitIgnoresPath(repoRoot, rel) {
+  return spawnSync5("git", ["check-ignore", "-q", "--", rel], { cwd: repoRoot, encoding: "utf8", timeout: 5e3 }).status === 0;
+}
+function bmadManifestGapDetail(repoRoot) {
+  const path = "_bmad/_config/manifest.yaml";
+  const bmad = join12(repoRoot, "_bmad");
+  if (!existsSync8(bmad)) return path;
+  const present = (...segments) => {
+    try {
+      lstatSync10(join12(bmad, ...segments));
+      return true;
+    } catch {
+      return false;
+    }
+  };
+  const record3 = `${path} (the installer's install record)`;
+  const remedy = `Restore it with: ${BMAD_SCAFFOLD_REMEDY}`;
+  if (!present("_config") && !present("core") && existsSync8(join12(bmad, "config.yaml"))) {
+    return `${record3}. BMB setup's \`--also-remove _config\` cleanup is the likely cause: it deletes all of _bmad/_config. ${remedy}`;
+  }
+  if (gitIgnoresPath(repoRoot, path)) return `${record3} is git-ignored in this checkout, so a fresh clone or worktree lacks it. ${remedy}`;
+  return `${record3} is missing. ${remedy}`;
+}
 function bmadSentinelGaps(repoRoot, modules = selectedBmadModules(repoRoot)) {
   const bmad = join12(repoRoot, "_bmad");
   const gaps = [];
   const absent = (...segments) => !existsSync8(join12(bmad, ...segments));
+  const installed = existsSync8(bmad);
   if (absent("config.toml")) gaps.push({ path: "config.toml", detail: "_bmad/config.toml" });
   for (const script of BMAD_RUNTIME_SCRIPT_SENTINELS) {
-    if (absent("scripts", script)) gaps.push({ path: join12("scripts", script), detail: `_bmad/scripts/${script}` });
+    if (!absent("scripts", script)) continue;
+    const rel = `_bmad/scripts/${script}`;
+    const detail = !installed ? rel : gitIgnoresPath(repoRoot, rel) ? `${rel} (git-ignored in this checkout, so a fresh clone or worktree lacks it; restore it with: ${BMAD_SCAFFOLD_REMEDY})` : `${rel} (restore it with: ${BMAD_SCAFFOLD_REMEDY})`;
+    gaps.push({ path: join12("scripts", script), detail });
   }
   if (absent("_config", "manifest.yaml")) {
-    gaps.push({
-      path: join12("_config", "manifest.yaml"),
-      detail: existsSync8(bmad) ? "_bmad/_config/manifest.yaml (the installer's install record). BMB setup's `--also-remove _config` cleanup is the likely cause: it deletes all of _bmad/_config. Restore it with: pj migrate bmad.scaffold" : "_bmad/_config/manifest.yaml"
-    });
+    gaps.push({ path: join12("_config", "manifest.yaml"), detail: bmadManifestGapDetail(repoRoot) });
   }
   let consolidated;
   for (const module of modules) {
@@ -13281,11 +13426,14 @@ function createAgentHooksChecks() {
         const unsafe = retired.filter((path) => lstatIfPresent(path)?.isDirectory());
         const details = [...finding2.details, ...wiring, ...registryBlocked, ...retired.map((path) => unsafe.includes(path) ? `Inspect and preserve retired script directory: ${path}` : `${path} is a retired skill writer`)];
         const miseDrift = mise !== null && upsertLinkAgentfilesBlock(mise, ctx) !== mise;
+        const { findings: auditFindings, pendingChanges, ...audited } = finding2;
+        const problems = auditFindings + wiring.length + registryBlocked.length + retired.length;
+        const summary = problems ? `${problems} Skillex finding(s)${pendingChanges ? `, ${pendingChanges} pending change(s)` : ""}` : pendingChanges && audited.status !== "pass" ? `${pendingChanges} pending Skillex change(s)` : audited.summary;
         return {
-          ...finding2,
-          status: wiring.length || retired.length || registryBlocked.length ? "fail" : finding2.status,
-          fixable: unsafe.length ? false : finding2.fixable || wiring.length > 0 || retired.length > 0 || miseDrift,
-          summary: details.length ? `${details.length} Skillex finding(s)` : finding2.summary,
+          ...audited,
+          status: wiring.length || retired.length || registryBlocked.length ? "fail" : audited.status,
+          fixable: unsafe.length ? false : audited.fixable || wiring.length > 0 || retired.length > 0 || miseDrift,
+          summary,
           details
         };
       },
@@ -13858,24 +14006,52 @@ function withInstallerSkillHandoff(check) {
     }
   };
 }
-function withScaffoldPostcondition(check) {
+function withScaffoldScriptRestore(check) {
   if (check.id !== "bmad.scaffold") return check;
   return {
     ...check,
     migrate: async (ctx, finding2) => {
-      const result2 = await check.migrate(ctx, finding2);
-      if (ctx.dryRun || result2.status !== "applied" && result2.status !== "noop") return result2;
-      const after = await check.audit(ctx);
-      if (after.status === "pass" || after.status === "skip") return result2;
-      return {
-        ...result2,
-        status: "partial",
-        summary: after.summary,
-        details: [...result2.details, `still failing after the install: ${after.summary}`, ...after.details]
-      };
+      const attempt = restoreScaffoldScripts(ctx, finding2);
+      if (attempt.result) return attempt.result;
+      const viaInstaller = await check.migrate(ctx, finding2);
+      return attempt.note ? { ...viaInstaller, details: [attempt.note, ...viaInstaller.details] } : viaInstaller;
     }
   };
 }
+function restoreScaffoldScripts(ctx, finding2) {
+  const manifest = manifestBmadModules(ctx.repoRoot);
+  if (manifest.status === "invalid") return {};
+  const modules = manifest.status === "valid" ? manifest.modules : configuredBmadModuleSelection(ctx.repoRoot)?.modules ?? [...DEFAULT_BMAD_MODULES];
+  const issues = bmadScaffoldIssues(ctx.repoRoot, modules);
+  const scriptGap = (path) => BMAD_RUNTIME_SCRIPT_SENTINELS.some((script) => path === join12("scripts", script));
+  if (!issues.gaps.length || issues.nameIssues.details.length || !issues.gaps.every((gap) => scriptGap(gap.path))) return {};
+  const state = bmadSetupScriptsState(ctx.repoRoot);
+  if (state.kind === "present") return {};
+  if (state.kind !== "missing") {
+    return { note: `targeted _bmad/scripts restore not possible, so this takes the installer path: ${state.kind === "decline" ? state.summary : state.error}` };
+  }
+  const source = `bmad-method@${BMAD_INSTALLER_VERSION} (${state.pkg.root})`;
+  if (ctx.dryRun) {
+    return { result: {
+      id: finding2.id,
+      title: finding2.title,
+      status: "applied",
+      summary: "Would restore the missing _bmad/scripts from the verified pinned bmad-method package (no reinstall)",
+      changedFiles: state.files,
+      details: [source]
+    } };
+  }
+  const applied = applyBmadSetupScripts(ctx.repoRoot, state.pkg, BMAD_INSTALLER_VERSION);
+  if (applied.error) return { note: `targeted _bmad/scripts restore failed, so this takes the installer path: ${applied.error}` };
+  return { result: {
+    id: finding2.id,
+    title: finding2.title,
+    status: applied.files.length ? "applied" : "noop",
+    summary: applied.files.length ? "Restored the missing _bmad/scripts from the verified pinned bmad-method package (no reinstall)" : "No changes required",
+    changedFiles: applied.files,
+    details: [source]
+  } };
+}
 function createBmadChecks() {
   return [
     {
@@ -14403,7 +14579,7 @@ function createBmadChecks() {
         };
       }
     }
-  ].map(withInstallerSkillHandoff).map(withScaffoldPostcondition);
+  ].map(withInstallerSkillHandoff).map(withScaffoldScriptRestore);
 }
 function createProjectMomoChecks() {
   return [
@@ -14614,16 +14790,17 @@ function formatAuditReport(report) {
 }
 function formatMigrationReport(report) {
   const idWidth = report.results.reduce((width, result2) => Math.max(width, result2.id.length), 0);
-  const blocked = report.results.filter((result2) => result2.status === "blocked").length;
-  const partial = report.results.filter((result2) => result2.status === "partial").length;
-  const overall = report.ok ? `${green(glyph.pass)} ${bold(report.dryRun ? "Migration preview complete" : "Migration complete")}` : blocked ? `${red(glyph.fail)} ${bold("Migration finished with blockers")}` : `${yellow(glyph.warn)} ${bold(`Migration incomplete  ${glyph.dot}  ${partial} rule${partial === 1 ? "" : "s"} still failing`)}`;
+  const advisory = report.results.filter((result2) => result2.advisory).length;
+  const blocked = report.results.filter((result2) => result2.status === "blocked" && !result2.advisory).length;
+  const partial = report.results.filter((result2) => result2.status === "partial" && !result2.advisory).length;
+  const overall = report.ok ? `${green(glyph.pass)} ${bold(report.dryRun ? "Migration preview complete" : "Migration complete")}${advisory ? `  ${dim(glyph.dot)}  ${yellow(`${advisory} warning${advisory === 1 ? "" : "s"}`)}` : ""}` : blocked ? `${red(glyph.fail)} ${bold("Migration finished with blockers")}` : `${yellow(glyph.warn)} ${bold(`Migration incomplete  ${glyph.dot}  ${partial} rule${partial === 1 ? "" : "s"} still failing`)}`;
   const lines = [""];
   lines.push(`  ${overall}${report.dryRun ? `  ${dim(glyph.dot)}  ${yellow("dry run")}` : ""}`);
   lines.push(`  ${dim(report.repo)}`);
   if (report.selectedRules.length) lines.push(`  ${dim(`rules: ${report.selectedRules.join(", ")}`)}`);
   lines.push("");
   for (const result2 of report.results) {
-    const style = statusStyle(result2.status);
+    const style = result2.advisory ? { ...statusStyle("warn"), label: `warning, ${result2.status}` } : statusStyle(result2.status);
     lines.push(`  ${style.color(style.glyph)}  ${style.color(result2.id.padEnd(idWidth))}  ${result2.summary}  ${dim(`[${style.label}]`)}`);
     for (const detail of result2.details) lines.push(`     ${dim(glyph.arrow)} ${dim(detail)}`);
     for (const file of result2.changedFiles) lines.push(`     ${green(glyph.add)} ${file}`);
@@ -14637,6 +14814,9 @@ function formatMigrationReport(report) {
   if (unresolved) {
     lines.push("");
     lines.push(`  ${dim(`Run \`pjangler audit\` for the full detail on the ${unresolved} rule${unresolved === 1 ? "" : "s"} still failing.`)}`);
+  } else if (advisory) {
+    lines.push("");
+    lines.push(`  ${dim(`${advisory} rule${advisory === 1 ? "" : "s"} could not finish but only warn${advisory === 1 ? "s" : ""}; they do not block. \`pjangler audit\` has the detail.`)}`);
   }
   lines.push("");
   return lines.join("\n");
@@ -15106,6 +15286,7 @@ function ticketScope(ticket) {
 }
 
 // src/recipes/ProjectRecipe.ts
+init_manifestIndex();
 init_tree_diff();
 
 // src/recipes/NotebookRecipe.ts
@@ -17172,6 +17353,17 @@ function unsafeToRemove(targetDir) {
   }
   return null;
 }
+function manifestRefusal(manifestPath) {
+  if (!existsSync18(manifestPath)) return void 0;
+  try {
+    const parsed = JSON.parse(readFileSync23(manifestPath, "utf8"));
+    if (!parsed || typeof parsed !== "object" || Array.isArray(parsed)) return `Expected a JSON object: ${manifestPath}`;
+    validateManifestShape(parsed, manifestPath);
+    return void 0;
+  } catch (error) {
+    return error instanceof SyntaxError ? `Malformed JSON: ${manifestPath}` : error instanceof Error ? error.message : String(error);
+  }
+}
 function publicAudit(report) {
   return {
     ...report,
@@ -17297,6 +17489,8 @@ var ProjectRecipe = class extends Recipe {
       });
     };
     let migrationReport;
+    let unfinishedMigrations = [];
+    const warnings = [];
     let audit;
     let notebookPlan;
     let notebookRecipeForCommit;
@@ -17396,20 +17590,37 @@ var ProjectRecipe = class extends Recipe {
           normalized.selectedRuleIds
         ));
         changedFiles.push(...migrationReport.changedFiles);
-        phases.push(...migrationReport.results.map((result2) => ({
+        const migrationPhases = migrationReport.results.map((result2) => ({
           id: result2.id,
           status: result2.status === "applied" ? "changed" : result2.status === "noop" ? "unchanged" : result2.status === "skipped" ? "skipped" : "failed",
           // A `partial` failed, but its writes really happened, so they stay
           // accounted for rather than vanishing from the transaction record.
           changedFiles: result2.status === "applied" || result2.status === "partial" ? result2.changedFiles : [],
           message: result2.summary
-        })));
-        errors.push(...migrationReport.results.filter((result2) => result2.status === "blocked" || result2.status === "partial").map((result2) => describeFinding(result2)));
+        }));
+        phases.push(...migrationPhases);
+        unfinishedMigrations = migrationReport.results.map((result2, index) => ({ result: result2, phase: migrationPhases[index] })).filter(({ result: result2 }) => result2.status === "blocked" || result2.status === "partial");
       }
       const eligibilityAudit = errors.length === 0 ? publicAudit(await this.registry.auditRecipes({ ...transactionContext, dryRun: true })) : void 0;
       audit = eligibilityAudit;
+      const gating = new Set((eligibilityAudit?.rules ?? []).filter((finding2) => gatesProject(finding2)).map((finding2) => finding2.id));
+      const reportedByMigration = /* @__PURE__ */ new Set();
+      for (const { result: result2, phase } of unfinishedMigrations) {
+        if (!eligibilityAudit || gating.has(result2.id)) {
+          errors.push(describeFinding(result2));
+          reportedByMigration.add(result2.id);
+        } else {
+          result2.advisory = true;
+          phase.status = "skipped";
+          phase.message = `advisory (does not block init): ${result2.summary}`;
+          warnings.push(`${result2.id}: ${result2.summary}`);
+        }
+      }
+      if (migrationReport && unfinishedMigrations.length && !unfinishedMigrations.some(({ result: result2 }) => !result2.advisory)) {
+        migrationReport.ok = true;
+      }
       if (eligibilityAudit && !eligibilityAudit.ok) {
-        errors.push(...eligibilityAudit.rules.filter((finding2) => gatesProject(finding2)).map((finding2) => describeFinding(finding2)));
+        errors.push(...eligibilityAudit.rules.filter((finding2) => gatesProject(finding2) && !reportedByMigration.has(finding2.id)).map((finding2) => describeFinding(finding2)));
       }
       phases.push({
         id: "project.audit:eligibility",
@@ -17453,6 +17664,13 @@ var ProjectRecipe = class extends Recipe {
           }
         }
       }
+      if (errors.length === 0) {
+        const refusal = manifestRefusal(join25(targetDir, ".project.json"));
+        if (refusal) {
+          errors.push(`manifest refused before external effects: ${refusal}`);
+          phases.push({ id: "project.manifest:validate", status: "failed", changedFiles: [], message: refusal });
+        }
+      }
       registryFinalizerEligible = errors.length === 0;
       if (errors.length === 0 && externalPlanActions.length) {
         const dispatching = externalPlanActions.some((action) => action.kind === "ticket-provider.create-or-link" && action.enabled);
@@ -17624,6 +17842,7 @@ var ProjectRecipe = class extends Recipe {
       selectedOperations: normalized.selectedOperations ?? [],
       selectedParityRules: normalized.selectedRuleIds ?? [],
       migrationReport,
+      warnings,
       ...bmadCompanion ? { bmadCompanion } : {}
     };
   }

package/dist/mcp-server.js

@@ -430,9 +430,44 @@ var init_notebookSettingsValidation = __esm({
 });
 
 // src/project/executionBinding.ts
+function executionReadiness(manifest) {
+  const execution = manifest.execution;
+  if (!execution || execution.mode === "legacy") return [];
+  const errors = [];
+  if (!["shadow", "managed"].includes(execution.mode)) errors.push("execution.mode must be legacy, shadow or managed");
+  if (!manifest.project_id) errors.push("canonical project_id missing");
+  if (manifest.ticket_provider?.type !== "plane" || !manifest.ticket_provider.workspace || !manifest.ticket_provider.board_id) errors.push("exact Plane binding missing");
+  if (execution.policy_version !== 2 || !execution.skill_version) errors.push("execution policy or skill pin missing");
+  for (const lane of EXECUTION_LANES) if (!execution.states?.[lane]) errors.push(`lane binding missing: ${lane}`);
+  for (const pin of ["pilot_bundle_sha256", "momo_bundle_sha256"]) if (!/^[a-f0-9]{64}$/.test(execution[pin] ?? "")) errors.push(`${pin} missing`);
+  if (!execution.working_label) errors.push("working label binding missing");
+  if (!execution.actors?.[execution.pm_actor] || execution.actors[execution.pm_actor].role !== "pm") errors.push("PM actor enrollment missing");
+  if (!execution.actors?.[execution.controller_actor] || execution.actors[execution.controller_actor].role !== "operator") errors.push("controller repair actor enrollment missing");
+  const ids = /* @__PURE__ */ new Set();
+  for (const [name, actor] of Object.entries(execution.actors ?? {})) {
+    if (!actor.native_user_id || !actor.key_ref?.startsWith("op://") || !actor.runtime_id) errors.push(`actor ${name}: native identity, op reference and runtime required`);
+    if (ids.has(actor.native_user_id)) errors.push(`actor ${name}: duplicate native identity`);
+    ids.add(actor.native_user_id);
+    if (!["pm", "operator", "reviewer", "interactive"].includes(actor.role)) errors.push(`actor ${name}: invalid role`);
+    if (name === execution.pm_actor && (!Array.isArray(actor.runtime?.planner_argv) || !actor.runtime.planner_argv.length || actor.runtime.planner_argv.some((x) => typeof x !== "string" || !x || x.includes("\0")))) errors.push("PM planner argv missing");
+    if (actor.runtime?.adapter !== "systemd" || !/^[a-zA-Z0-9_-]+$/.test(actor.runtime?.unit_prefix ?? "")) errors.push(`actor ${name}: supervised runtime missing`);
+  }
+  if (execution.legacy_writers_fenced !== true) errors.push("legacy writers not fenced");
+  return errors;
+}
+function validateExecutionBinding(manifest) {
+  if (!manifest.execution) return;
+  if (typeof manifest.execution !== "object" || Array.isArray(manifest.execution)) throw new Error("execution must be an object");
+  if (manifest.execution.mode === "managed") {
+    const errors = executionReadiness(manifest);
+    if (errors.length) throw new Error(`Managed execution not ready: ${errors.join("; ")}`);
+  } else if (!["legacy", "shadow"].includes(manifest.execution.mode)) throw new Error("invalid execution mode");
+}
+var EXECUTION_LANES;
 var init_executionBinding = __esm({
   "src/project/executionBinding.ts"() {
     "use strict";
+    EXECUTION_LANES = ["Backlog", "Needs Re-evaluation", "Todo", "In Progress", "E2E Testing & QA", "Ready for Documentation", "Done", "Needs Attention", "Cancelled"];
   }
 });
 
@@ -445,6 +480,46 @@ function normalizeProjectId2(value) {
     throw new RegistryError(error instanceof Error ? error.message : String(error));
   }
 }
+function object(value) {
+  return !!value && typeof value === "object" && !Array.isArray(value);
+}
+function validateManifestShape(manifest, path) {
+  validateExecutionBinding(manifest);
+  const fail = (field2, shape) => {
+    throw new RegistryError(`Manifest ${path}: ${field2} must be ${shape}`);
+  };
+  const strings = (value, names, prefix = "") => {
+    for (const name of names) if (value[name] !== void 0 && typeof value[name] !== "string") fail(`${prefix}${name}`, "a string");
+  };
+  strings(manifest, ["project_name", "name", "project_description", "description", "status", "repo_path", "created_at", "updated_at"]);
+  for (const field2 of ["ticket_provider", "agents", "template", "notebook", "automation"]) if (manifest[field2] !== void 0 && !object(manifest[field2])) fail(field2, "an object");
+  if (manifest.source_artifacts !== void 0 && !Array.isArray(manifest.source_artifacts)) fail("source_artifacts", "an array");
+  for (const [index, artifact] of (manifest.source_artifacts ?? []).entries()) {
+    if (!object(artifact)) fail(`source_artifacts.${index}`, "an object");
+    strings(artifact, ["kind", "path", "package_name"], `source_artifacts.${index}.`);
+  }
+  if (manifest.ticket_provider) strings(manifest.ticket_provider, ["type", "workspace", "identifier", "identifier_source", "identifier_fetched_at", "board_id", "board_confirmed_at", "board_url", "state", "scope_label"], "ticket_provider.");
+  if (manifest.ticket_provider?.scope_default !== void 0 && typeof manifest.ticket_provider.scope_default !== "boolean") fail("ticket_provider.scope_default", "a boolean");
+  for (const [name, agent] of Object.entries(manifest.agents ?? {})) {
+    if (!object(agent)) fail(`agents.${name}`, "an object");
+    strings(agent, ["role", "role_dir", "provisioning_state"], `agents.${name}.`);
+  }
+  if (manifest.template?.commonproject !== void 0) {
+    if (!object(manifest.template.commonproject)) fail("template.commonproject", "an object");
+    const template = manifest.template.commonproject;
+    if (template.enabled !== void 0 && typeof template.enabled !== "boolean") fail("template.commonproject.enabled", "boolean");
+    strings(template, ["primary_language", "project_type"], "template.commonproject.");
+  }
+  for (const field2 of ["binding", "policy"]) if (manifest.notebook?.[field2] !== void 0 && !object(manifest.notebook[field2])) fail(`notebook.${field2}`, "an object");
+  if (manifest.notebook?.binding) strings(manifest.notebook.binding, ["provider", "state", "notebook_name", "blocked_reason", "notebook_id", "overview_note_id", "created_at", "updated_at"], "notebook.binding.");
+  if (manifest.notebook?.policy) {
+    try {
+      validateGlobalNotebookConfig({ defaults: manifest.notebook.policy });
+    } catch (error) {
+      throw new RegistryError(`Manifest ${path}: invalid notebook policy: ${String(error)}`);
+    }
+  }
+}
 function recordFromManifest(manifest, path) {
   const id = normalizeProjectId2(manifest.project_id ?? manifest.project_slug);
   const { project_slug: _old, project_name: _name, project_description: _description, notebook, ...rest } = manifest;
@@ -1512,12 +1587,40 @@ function resolveSourceSkillPath(sourceSkill, env2 = process.env) {
   const hint = `${searched} Add project-specific roots with ${PROJECT_SOURCE_SKILL_ROOTS_ENV}.`;
   throw new Error(`Source skill not found: ${sourceSkill}.${hint}`);
 }
+function looksLikePath(value) {
+  return /^(?:\/|~\/|\.{1,2}\/)/.test(value);
+}
+function normalizeLegacyManifest(manifest) {
+  const artifacts = manifest.source_artifacts;
+  if (!Array.isArray(artifacts)) return { manifest, notes: [] };
+  const notes = [];
+  const normalized = artifacts.map((artifact, index) => {
+    if (typeof artifact !== "string" || !looksLikePath(artifact)) return artifact;
+    notes.push(`.project.json source_artifacts.${index}: bare path normalized to {"kind": "${LEGACY_SOURCE_ARTIFACT_KIND}", "path": "${artifact}"}`);
+    return { kind: LEGACY_SOURCE_ARTIFACT_KIND, path: artifact };
+  });
+  return notes.length ? { manifest: { ...manifest, source_artifacts: normalized }, notes } : { manifest, notes };
+}
 function planProjectInit(input) {
   if (!input.name.trim()) throw new Error("Project name is required");
   const targetDir = resolve10(input.targetDir ?? defaultProjectTargetDir(input.name, input.cwd));
   const localManifestPath = join17(targetDir, ".project.json");
   const localManifestContent = existsSync11(localManifestPath) ? readFileSync15(localManifestPath, "utf8") : void 0;
-  const localManifest = localManifestContent === void 0 ? void 0 : JSON.parse(localManifestContent);
+  let localManifest;
+  const manifestNotes = [];
+  if (localManifestContent !== void 0) {
+    let parsed;
+    try {
+      parsed = JSON.parse(localManifestContent);
+    } catch {
+      throw new Error(`Malformed JSON: ${localManifestPath}`);
+    }
+    if (!parsed || typeof parsed !== "object" || Array.isArray(parsed)) throw new Error(`Expected a JSON object: ${localManifestPath}`);
+    const normalized = normalizeLegacyManifest(parsed);
+    localManifest = normalized.manifest;
+    manifestNotes.push(...normalized.notes);
+    validateManifestShape(localManifest, localManifestPath);
+  }
   const localId = localManifest?.project_id ?? localManifest?.project_slug;
   const slug = normalizeProjectId(input.projectSlug ?? localId ?? slugifyProjectName(input.name));
   if (localId && normalizeProjectId(localId) !== slug) throw new Error(`Project ID ${slug} conflicts with authoritative manifest ${localId}`);
@@ -1612,6 +1715,7 @@ function planProjectInit(input) {
   validateNoDuplicateProject(registry, project, overwrite);
   const pjanglerRoot = resolve10(input.pjanglerRoot ?? resolvePjanglerRoot());
   const manifest = projectManifestFromRegistryProject(project);
+  validateManifestShape(manifest, localManifestPath);
   const apply = input.apply ?? false;
   const live = input.live ?? false;
   const provisionTicketBoard = input.provisionTicketBoard ?? true;
@@ -1667,7 +1771,7 @@ function planProjectInit(input) {
     project,
     manifest,
     actions,
-    ...input.boardUrl !== void 0 ? { warnings: [BOARD_URL_DEPRECATION_WARNING] } : {}
+    ...input.boardUrl !== void 0 || manifestNotes.length ? { warnings: [...input.boardUrl !== void 0 ? [BOARD_URL_DEPRECATION_WARNING] : [], ...manifestNotes] } : {}
   };
 }
 function linkTicketProviderBoard(plan, action, boardId, identifier, now = /* @__PURE__ */ new Date()) {
@@ -2016,7 +2120,7 @@ function expandHome(path) {
 function isRecord2(value) {
   return typeof value === "object" && value !== null && !Array.isArray(value);
 }
-var PROJECT_SOURCE_SKILL_ROOTS_ENV, TICKET_PROVIDER_ADAPTERS_ENV, PROJECT_REGISTRY_SCHEMA_VERSION, DEFAULT_NEW_PROJECT_STATUS, PROJECT_TYPES, PROJECT_TYPE_LANGUAGES, PROJECT_TYPE_SENTINELS, BOARD_URL_DEPRECATION_WARNING, PROJECT_IDENTIFIER_SOURCES, IDENTIFIER_ASSIGNING_PROVIDERS, TICKET_PROVIDER_STATES, IDENTIFIER_REPAIR_COMMAND, DEFAULT_SOURCE_SKILL_ROOTS, PROJECT_REGISTRY_OWNED_KEYS, PROJECT_NOTEBOOK_OWNED_KEYS, TICKET_PROVIDER_OWNED_KEYS, GLOBAL_NOTEBOOK_OWNED_KEYS, GLOBAL_NOTEBOOK_AUTH_OWNED_KEYS, GLOBAL_NOTEBOOK_DEFAULTS_OWNED_KEYS, GLOBAL_NOTEBOOK_LIMITS_OWNED_KEYS, GLOBAL_NOTEBOOK_SUMMARIZER_OWNED_KEYS, SAFE_PATH_SEGMENT;
+var PROJECT_SOURCE_SKILL_ROOTS_ENV, TICKET_PROVIDER_ADAPTERS_ENV, PROJECT_REGISTRY_SCHEMA_VERSION, DEFAULT_NEW_PROJECT_STATUS, PROJECT_TYPES, PROJECT_TYPE_LANGUAGES, PROJECT_TYPE_SENTINELS, BOARD_URL_DEPRECATION_WARNING, PROJECT_IDENTIFIER_SOURCES, IDENTIFIER_ASSIGNING_PROVIDERS, TICKET_PROVIDER_STATES, IDENTIFIER_REPAIR_COMMAND, DEFAULT_SOURCE_SKILL_ROOTS, PROJECT_REGISTRY_OWNED_KEYS, PROJECT_NOTEBOOK_OWNED_KEYS, TICKET_PROVIDER_OWNED_KEYS, GLOBAL_NOTEBOOK_OWNED_KEYS, GLOBAL_NOTEBOOK_AUTH_OWNED_KEYS, GLOBAL_NOTEBOOK_DEFAULTS_OWNED_KEYS, GLOBAL_NOTEBOOK_LIMITS_OWNED_KEYS, GLOBAL_NOTEBOOK_SUMMARIZER_OWNED_KEYS, SAFE_PATH_SEGMENT, LEGACY_SOURCE_ARTIFACT_KIND;
 var init_project = __esm({
   "src/project/index.ts"() {
     "use strict";
@@ -2072,6 +2176,7 @@ var init_project = __esm({
     GLOBAL_NOTEBOOK_LIMITS_OWNED_KEYS = Object.keys(DEFAULT_NOTEBOOK_LIMITS);
     GLOBAL_NOTEBOOK_SUMMARIZER_OWNED_KEYS = ["executable", "args"];
     SAFE_PATH_SEGMENT = /^[A-Za-z0-9](?:[A-Za-z0-9._-]*[A-Za-z0-9])?$/;
+    LEGACY_SOURCE_ARTIFACT_KIND = "reference";
   }
 });
 
@@ -5585,6 +5690,10 @@ function backupToSnapshot(backup) {
   }
   return snapshot;
 }
+function removeEntry(full, stat) {
+  if (stat.isDirectory() && !stat.isSymbolicLink()) rmSync(full, { recursive: true, force: true });
+  else unlinkSync(full);
+}
 function restoreSingleEntry(root, rel, entry) {
   const full = rel === "." ? root : join3(root, rel);
   let currentStat;
@@ -5595,7 +5704,7 @@ function restoreSingleEntry(root, rel, entry) {
   }
   if (entry.kind === "dir") {
     if (currentStat && (!currentStat.isDirectory() || currentStat.isSymbolicLink())) {
-      rmSync(full, { recursive: true, force: true });
+      removeEntry(full, currentStat);
       currentStat = void 0;
     }
     if (!currentStat) mkdirSync2(full, { recursive: true });
@@ -5606,7 +5715,7 @@ function restoreSingleEntry(root, rel, entry) {
   if (entry.kind === "link") {
     if (currentStat) {
       if (currentStat.isSymbolicLink() && readlinkSync2(full) === entry.target) return;
-      rmSync(full, { recursive: true, force: true });
+      removeEntry(full, currentStat);
     }
     symlinkSync(entry.target, full);
     return;
@@ -5615,7 +5724,7 @@ function restoreSingleEntry(root, rel, entry) {
     if ((currentStat.mode & 4095) === entry.mode && readFileSync2(full).equals(entry.bytes)) return;
     unlinkSync(full);
   } else if (currentStat) {
-    rmSync(full, { recursive: true, force: true });
+    removeEntry(full, currentStat);
   }
   writeFileSync2(full, entry.bytes);
   chmodSync(full, entry.mode);
@@ -6224,10 +6333,10 @@ function openDisplacedStash(projectRoot) {
           index.push({ rel, kind: "link", target });
           count++;
         } else if (bytes) {
-          const object = createHash4("sha256").update(bytes).digest("hex");
-          const objectPath = join5(open(), "objects", object);
+          const object2 = createHash4("sha256").update(bytes).digest("hex");
+          const objectPath = join5(open(), "objects", object2);
           if (!existsSync3(objectPath)) writeFileSync3(objectPath, bytes);
-          index.push({ rel, kind: "file", mode: stat.mode & 4095, object });
+          index.push({ rel, kind: "file", mode: stat.mode & 4095, object: object2 });
           count++;
         } else if (stat.isDirectory()) {
           open();
@@ -8196,9 +8305,13 @@ async function predictRootCollisions(ctx, incoming) {
 async function auditProjectSkills(ctx) {
   const result2 = await inspectStatus(skillCoreOptions(ctx));
   const details = skillDiagnostics(result2.findings);
+  let findings = result2.findings.filter((finding2) => finding2.severity !== "info").length;
   details.push(...(result2.data?.changes ?? []).map((change) => `${change.action}: ${change.path}`));
+  const pendingChanges = (result2.data?.changes ?? []).length;
   const plan = planSkillRoots(ctx.repoRoot);
-  details.push(...skillRootsSummary(plan));
+  const rootLines = skillRootsSummary(plan);
+  details.push(...rootLines);
+  findings += rootLines.length;
   const conflict = activationConflict(ctx, result2.findings);
   let conflictResolvable = false;
   if (conflict?.kind === "alias") conflictResolvable = plan.clean;
@@ -8206,6 +8319,7 @@ async function auditProjectSkills(ctx) {
     const predictions = await predictRootCollisions(ctx, []);
     conflictResolvable = predictions.length > 0 && predictions.every(({ decision }) => decision.action !== "block");
     for (const { decision } of predictions) {
+      if (decision.action === "block") findings += 1;
       details.push(decision.action === "block" ? `blocked: ${decision.detail}` : `resolvable root collision: ${decision.detail.replace(/^replaced/, "replace")}`);
     }
   }
@@ -8214,7 +8328,10 @@ async function auditProjectSkills(ctx) {
   const installerOnly = errors.length > 0 && await installerRefusalsResolvable(ctx, errors, handoff);
   if (installerOnly) details.push("resolvable: every refusal is at a skill the bmad-method installer provides; migrate excludes the inherited selection and releases the replaced links");
   if (handoff.skipped) details.push(`installer skill handoff unavailable: ${handoff.skipped}`);
-  if (handoff.restored.length) details.push(...handoff.restored.map((name) => `stale exclusion: ${name} was excluded for the bmad-method installer's copy, which is gone; migrate restores the inherited catalog skill`));
+  if (handoff.restored.length) {
+    findings += handoff.restored.length;
+    details.push(...handoff.restored.map((name) => `stale exclusion: ${name} was excluded for the bmad-method installer's copy, which is gone; migrate restores the inherited catalog skill`));
+  }
   if (result2.exit === 2 || result2.exit === 3) details.push(migrationGuidance(ctx));
   const changes = result2.data?.changes ?? [];
   const receiptOnly = result2.exit === 6 && changes.length > 0 && changes.every((change) => change.action === "write-receipt") && !result2.findings.some((finding2) => finding2.severity === "error");
@@ -8226,6 +8343,8 @@ async function auditProjectSkills(ctx) {
     status: result2.exit === 0 ? staleHandoff ? "warn" : "pass" : result2.exit === 4 || receiptOnly ? "warn" : "fail",
     summary: result2.exit === 0 ? "Skillex declaration and activation are in parity" : receiptOnly ? "Skillex activation is in parity; its receipt predates the current catalog commit" : `Skillex inspection returned exit ${result2.exit}`,
     details,
+    findings,
+    pendingChanges,
     fixable: result2.exit === 0 || result2.exit === 6 || conflictResolvable || installerOnly || staleHandoff || result2.findings.some((finding2) => finding2.code === "E_NO_PROJECT_MANIFEST")
   };
 }
@@ -11267,28 +11386,54 @@ function consolidatedBmadConfig(repoRoot) {
   if (!existsSync8(path)) return { status: "absent" };
   let parsed;
   try {
-    parsed = YAML4.parse(readText(path));
+    parsed = YAML4.parse(readText(path), { uniqueKeys: false });
   } catch (error) {
-    return { status: "unusable", reason: `could not be parsed: ${error instanceof Error ? error.message.split("\n")[0] : String(error)}` };
+    const reason = error instanceof Error ? error.message.split("\n")[0].replace(/:\s*$/, "") : String(error);
+    return { status: "unusable", reason: `could not be parsed: ${reason}` };
   }
   if (!parsed || typeof parsed !== "object" || Array.isArray(parsed)) {
     return { status: "unusable", reason: "is not a YAML mapping" };
   }
   return { status: "mapping", sections: new Set(Object.keys(parsed)) };
 }
+var BMAD_SCAFFOLD_REMEDY = "pj migrate bmad.scaffold";
+function gitIgnoresPath(repoRoot, rel) {
+  return spawnSync5("git", ["check-ignore", "-q", "--", rel], { cwd: repoRoot, encoding: "utf8", timeout: 5e3 }).status === 0;
+}
+function bmadManifestGapDetail(repoRoot) {
+  const path = "_bmad/_config/manifest.yaml";
+  const bmad = join12(repoRoot, "_bmad");
+  if (!existsSync8(bmad)) return path;
+  const present = (...segments) => {
+    try {
+      lstatSync10(join12(bmad, ...segments));
+      return true;
+    } catch {
+      return false;
+    }
+  };
+  const record3 = `${path} (the installer's install record)`;
+  const remedy = `Restore it with: ${BMAD_SCAFFOLD_REMEDY}`;
+  if (!present("_config") && !present("core") && existsSync8(join12(bmad, "config.yaml"))) {
+    return `${record3}. BMB setup's \`--also-remove _config\` cleanup is the likely cause: it deletes all of _bmad/_config. ${remedy}`;
+  }
+  if (gitIgnoresPath(repoRoot, path)) return `${record3} is git-ignored in this checkout, so a fresh clone or worktree lacks it. ${remedy}`;
+  return `${record3} is missing. ${remedy}`;
+}
 function bmadSentinelGaps(repoRoot, modules = selectedBmadModules(repoRoot)) {
   const bmad = join12(repoRoot, "_bmad");
   const gaps = [];
   const absent = (...segments) => !existsSync8(join12(bmad, ...segments));
+  const installed = existsSync8(bmad);
   if (absent("config.toml")) gaps.push({ path: "config.toml", detail: "_bmad/config.toml" });
   for (const script of BMAD_RUNTIME_SCRIPT_SENTINELS) {
-    if (absent("scripts", script)) gaps.push({ path: join12("scripts", script), detail: `_bmad/scripts/${script}` });
+    if (!absent("scripts", script)) continue;
+    const rel = `_bmad/scripts/${script}`;
+    const detail = !installed ? rel : gitIgnoresPath(repoRoot, rel) ? `${rel} (git-ignored in this checkout, so a fresh clone or worktree lacks it; restore it with: ${BMAD_SCAFFOLD_REMEDY})` : `${rel} (restore it with: ${BMAD_SCAFFOLD_REMEDY})`;
+    gaps.push({ path: join12("scripts", script), detail });
   }
   if (absent("_config", "manifest.yaml")) {
-    gaps.push({
-      path: join12("_config", "manifest.yaml"),
-      detail: existsSync8(bmad) ? "_bmad/_config/manifest.yaml (the installer's install record). BMB setup's `--also-remove _config` cleanup is the likely cause: it deletes all of _bmad/_config. Restore it with: pj migrate bmad.scaffold" : "_bmad/_config/manifest.yaml"
-    });
+    gaps.push({ path: join12("_config", "manifest.yaml"), detail: bmadManifestGapDetail(repoRoot) });
   }
   let consolidated;
   for (const module of modules) {
@@ -12092,11 +12237,14 @@ function createAgentHooksChecks() {
         const unsafe = retired.filter((path) => lstatIfPresent(path)?.isDirectory());
         const details = [...finding2.details, ...wiring, ...registryBlocked, ...retired.map((path) => unsafe.includes(path) ? `Inspect and preserve retired script directory: ${path}` : `${path} is a retired skill writer`)];
         const miseDrift = mise !== null && upsertLinkAgentfilesBlock(mise, ctx) !== mise;
+        const { findings: auditFindings, pendingChanges, ...audited } = finding2;
+        const problems = auditFindings + wiring.length + registryBlocked.length + retired.length;
+        const summary = problems ? `${problems} Skillex finding(s)${pendingChanges ? `, ${pendingChanges} pending change(s)` : ""}` : pendingChanges && audited.status !== "pass" ? `${pendingChanges} pending Skillex change(s)` : audited.summary;
         return {
-          ...finding2,
-          status: wiring.length || retired.length || registryBlocked.length ? "fail" : finding2.status,
-          fixable: unsafe.length ? false : finding2.fixable || wiring.length > 0 || retired.length > 0 || miseDrift,
-          summary: details.length ? `${details.length} Skillex finding(s)` : finding2.summary,
+          ...audited,
+          status: wiring.length || retired.length || registryBlocked.length ? "fail" : audited.status,
+          fixable: unsafe.length ? false : audited.fixable || wiring.length > 0 || retired.length > 0 || miseDrift,
+          summary,
           details
         };
       },
@@ -12669,24 +12817,52 @@ function withInstallerSkillHandoff(check) {
     }
   };
 }
-function withScaffoldPostcondition(check) {
+function withScaffoldScriptRestore(check) {
   if (check.id !== "bmad.scaffold") return check;
   return {
     ...check,
     migrate: async (ctx, finding2) => {
-      const result2 = await check.migrate(ctx, finding2);
-      if (ctx.dryRun || result2.status !== "applied" && result2.status !== "noop") return result2;
-      const after = await check.audit(ctx);
-      if (after.status === "pass" || after.status === "skip") return result2;
-      return {
-        ...result2,
-        status: "partial",
-        summary: after.summary,
-        details: [...result2.details, `still failing after the install: ${after.summary}`, ...after.details]
-      };
+      const attempt = restoreScaffoldScripts(ctx, finding2);
+      if (attempt.result) return attempt.result;
+      const viaInstaller = await check.migrate(ctx, finding2);
+      return attempt.note ? { ...viaInstaller, details: [attempt.note, ...viaInstaller.details] } : viaInstaller;
     }
   };
 }
+function restoreScaffoldScripts(ctx, finding2) {
+  const manifest = manifestBmadModules(ctx.repoRoot);
+  if (manifest.status === "invalid") return {};
+  const modules = manifest.status === "valid" ? manifest.modules : configuredBmadModuleSelection(ctx.repoRoot)?.modules ?? [...DEFAULT_BMAD_MODULES];
+  const issues = bmadScaffoldIssues(ctx.repoRoot, modules);
+  const scriptGap = (path) => BMAD_RUNTIME_SCRIPT_SENTINELS.some((script) => path === join12("scripts", script));
+  if (!issues.gaps.length || issues.nameIssues.details.length || !issues.gaps.every((gap) => scriptGap(gap.path))) return {};
+  const state = bmadSetupScriptsState(ctx.repoRoot);
+  if (state.kind === "present") return {};
+  if (state.kind !== "missing") {
+    return { note: `targeted _bmad/scripts restore not possible, so this takes the installer path: ${state.kind === "decline" ? state.summary : state.error}` };
+  }
+  const source = `bmad-method@${BMAD_INSTALLER_VERSION} (${state.pkg.root})`;
+  if (ctx.dryRun) {
+    return { result: {
+      id: finding2.id,
+      title: finding2.title,
+      status: "applied",
+      summary: "Would restore the missing _bmad/scripts from the verified pinned bmad-method package (no reinstall)",
+      changedFiles: state.files,
+      details: [source]
+    } };
+  }
+  const applied = applyBmadSetupScripts(ctx.repoRoot, state.pkg, BMAD_INSTALLER_VERSION);
+  if (applied.error) return { note: `targeted _bmad/scripts restore failed, so this takes the installer path: ${applied.error}` };
+  return { result: {
+    id: finding2.id,
+    title: finding2.title,
+    status: applied.files.length ? "applied" : "noop",
+    summary: applied.files.length ? "Restored the missing _bmad/scripts from the verified pinned bmad-method package (no reinstall)" : "No changes required",
+    changedFiles: applied.files,
+    details: [source]
+  } };
+}
 function createBmadChecks() {
   return [
     {
@@ -13214,7 +13390,7 @@ function createBmadChecks() {
         };
       }
     }
-  ].map(withInstallerSkillHandoff).map(withScaffoldPostcondition);
+  ].map(withInstallerSkillHandoff).map(withScaffoldScriptRestore);
 }
 function createProjectMomoChecks() {
   return [
@@ -13837,6 +14013,7 @@ function ticketScope(ticket) {
 }
 
 // src/recipes/ProjectRecipe.ts
+init_manifestIndex();
 init_tree_diff();
 
 // src/recipes/NotebookRecipe.ts
@@ -15666,6 +15843,17 @@ function unsafeToRemove(targetDir) {
   }
   return null;
 }
+function manifestRefusal(manifestPath) {
+  if (!existsSync18(manifestPath)) return void 0;
+  try {
+    const parsed = JSON.parse(readFileSync21(manifestPath, "utf8"));
+    if (!parsed || typeof parsed !== "object" || Array.isArray(parsed)) return `Expected a JSON object: ${manifestPath}`;
+    validateManifestShape(parsed, manifestPath);
+    return void 0;
+  } catch (error) {
+    return error instanceof SyntaxError ? `Malformed JSON: ${manifestPath}` : error instanceof Error ? error.message : String(error);
+  }
+}
 function publicAudit(report) {
   return {
     ...report,
@@ -15791,6 +15979,8 @@ var ProjectRecipe = class extends Recipe {
       });
     };
     let migrationReport;
+    let unfinishedMigrations = [];
+    const warnings = [];
     let audit;
     let notebookPlan;
     let notebookRecipeForCommit;
@@ -15890,20 +16080,37 @@ var ProjectRecipe = class extends Recipe {
           normalized.selectedRuleIds
         ));
         changedFiles.push(...migrationReport.changedFiles);
-        phases.push(...migrationReport.results.map((result2) => ({
+        const migrationPhases = migrationReport.results.map((result2) => ({
           id: result2.id,
           status: result2.status === "applied" ? "changed" : result2.status === "noop" ? "unchanged" : result2.status === "skipped" ? "skipped" : "failed",
           // A `partial` failed, but its writes really happened, so they stay
           // accounted for rather than vanishing from the transaction record.
           changedFiles: result2.status === "applied" || result2.status === "partial" ? result2.changedFiles : [],
           message: result2.summary
-        })));
-        errors.push(...migrationReport.results.filter((result2) => result2.status === "blocked" || result2.status === "partial").map((result2) => describeFinding(result2)));
+        }));
+        phases.push(...migrationPhases);
+        unfinishedMigrations = migrationReport.results.map((result2, index) => ({ result: result2, phase: migrationPhases[index] })).filter(({ result: result2 }) => result2.status === "blocked" || result2.status === "partial");
       }
       const eligibilityAudit = errors.length === 0 ? publicAudit(await this.registry.auditRecipes({ ...transactionContext, dryRun: true })) : void 0;
       audit = eligibilityAudit;
+      const gating = new Set((eligibilityAudit?.rules ?? []).filter((finding2) => gatesProject(finding2)).map((finding2) => finding2.id));
+      const reportedByMigration = /* @__PURE__ */ new Set();
+      for (const { result: result2, phase } of unfinishedMigrations) {
+        if (!eligibilityAudit || gating.has(result2.id)) {
+          errors.push(describeFinding(result2));
+          reportedByMigration.add(result2.id);
+        } else {
+          result2.advisory = true;
+          phase.status = "skipped";
+          phase.message = `advisory (does not block init): ${result2.summary}`;
+          warnings.push(`${result2.id}: ${result2.summary}`);
+        }
+      }
+      if (migrationReport && unfinishedMigrations.length && !unfinishedMigrations.some(({ result: result2 }) => !result2.advisory)) {
+        migrationReport.ok = true;
+      }
       if (eligibilityAudit && !eligibilityAudit.ok) {
-        errors.push(...eligibilityAudit.rules.filter((finding2) => gatesProject(finding2)).map((finding2) => describeFinding(finding2)));
+        errors.push(...eligibilityAudit.rules.filter((finding2) => gatesProject(finding2) && !reportedByMigration.has(finding2.id)).map((finding2) => describeFinding(finding2)));
       }
       phases.push({
         id: "project.audit:eligibility",
@@ -15947,6 +16154,13 @@ var ProjectRecipe = class extends Recipe {
           }
         }
       }
+      if (errors.length === 0) {
+        const refusal = manifestRefusal(join24(targetDir, ".project.json"));
+        if (refusal) {
+          errors.push(`manifest refused before external effects: ${refusal}`);
+          phases.push({ id: "project.manifest:validate", status: "failed", changedFiles: [], message: refusal });
+        }
+      }
       registryFinalizerEligible = errors.length === 0;
       if (errors.length === 0 && externalPlanActions.length) {
         const dispatching = externalPlanActions.some((action) => action.kind === "ticket-provider.create-or-link" && action.enabled);
@@ -16118,6 +16332,7 @@ var ProjectRecipe = class extends Recipe {
       selectedOperations: normalized.selectedOperations ?? [],
       selectedParityRules: normalized.selectedRuleIds ?? [],
       migrationReport,
+      warnings,
       ...bmadCompanion ? { bmadCompanion } : {}
     };
   }
@@ -17918,6 +18133,7 @@ function projectPreflightFailure(plan, errors, audit) {
     plan,
     mode: plan.actions.some((action) => action.kind === "copier.copy.commonproject") ? "create" : "sync",
     audit,
+    warnings: [],
     selectedOperations: plan.actions.map((action) => action.kind),
     selectedParityRules: []
   };

package/dist/project-registry-service.js

@@ -210,7 +210,7 @@ function mergeMissing(current, fallback) {
 function hash(data) {
   return createHash("sha256").update(data).digest("hex");
 }
-function validateManifestFields(manifest, path) {
+function validateManifestShape(manifest, path) {
   validateExecutionBinding(manifest);
   const fail = (field, shape) => {
     throw new RegistryError(`Manifest ${path}: ${field} must be ${shape}`);
@@ -269,7 +269,7 @@ async function readManifest(path) {
     throw new RegistryError(`Malformed JSON: ${path}`);
   }
   if (!object(manifest)) throw new RegistryError(`Expected a JSON object: ${path}`);
-  validateManifestFields(manifest, path);
+  validateManifestShape(manifest, path);
   const id = normalizeProjectId2(manifest.project_id ?? manifest.project_slug);
   if (manifest.project_id && manifest.project_slug && normalizeProjectId2(manifest.project_slug) !== id) {
     throw new RegistryError(`Conflicting project_id and project_slug: ${path}`, 409, "identity_conflict");
@@ -298,7 +298,7 @@ function recordFromManifest(manifest, path) {
   };
 }
 async function writeManifest(original, manifest) {
-  validateManifestFields(manifest, original.path);
+  validateManifestShape(manifest, original.path);
   const serialized = serializedManifest(manifest);
   const temp = join(dirname(original.path), `.project.json.${randomUUID()}.tmp`);
   let committed = false;
@@ -585,7 +585,7 @@ var ManifestIndex = class {
         else throw new RegistryError(`Missing concurrency baseline for ${id}; reload the registry and retry`, 409, "stale_manifest");
         if (next.repo_path !== current.repo_path) throw new RegistryError(`Cannot move ${id} through a registry snapshot; register its canonical manifest path`, 409, "identity_conflict");
         const manifest = applyRecord(read.manifest, current, next);
-        validateManifestFields(manifest, path);
+        validateManifestShape(manifest, path);
         serializedManifest(manifest);
         writes.push({ read, manifest, oldId: row?.project_id });
       }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@delorenj/pjangler",
-  "version": "1.5.53",
+  "version": "1.5.54",
   "description": "Project subsystem bootstrapper CLI",
   "type": "module",
   "main": "dist/index.js",