fix(stores): allow empty store registration

docs/agent-contract.md

@@ -97,13 +97,13 @@ setup/register: `{ "store": {id, root, metadata_path?}, "registry": {path, regis
 `no_openspec_root`, `no_root_with_registered_stores`, `no_registered_stores`, `unknown_store`, `store_identity_mismatch`, `unhealthy_store_root`, `store_path_not_supported`, `invalid_store_pointer`, `initiative_option_removed`, `areas_option_removed`; pass-through: `invalid_store_id`, `invalid_store_registry`, `invalid_store_metadata`.
 
 ### OpenSpec-root health (error, no fix)
-`openspec_store_root_missing`, `openspec_root_missing`, `openspec_config_missing`, `openspec_specs_missing`, `openspec_changes_missing`, `openspec_archive_missing`, plus `_not_directory` variants of each.
+`openspec_store_root_missing`, `openspec_store_root_not_directory`, `openspec_root_missing`, `openspec_root_not_directory`, `openspec_config_missing`, `openspec_config_not_file`, `openspec_specs_not_directory`, `openspec_changes_not_directory`, `openspec_archive_not_directory`. During the stores beta, `openspec/specs/`, `openspec/changes/`, and `openspec/changes/archive/` may be absent in a healthy root; they are only health errors when present but not directories.
 
 ### Store registry/identity/state
 `invalid_store_id`, `invalid_store_registry`, `invalid_store_metadata`, `store_registry_busy`, `store_not_found`, `no_store_registry`, `store_registry_changed`, `store_metadata_missing`, `store_metadata_id_mismatch`, `store_metadata_invalid`, `store_id_conflict`, `store_path_conflict`, `store_already_registered` (info).
 
 ### Store setup/register/remove
-`store_setup_id_required`, `store_setup_path_required`, `store_setup_path_not_directory`, `store_setup_inside_git_repo`, `store_setup_non_empty_directory`, `store_setup_cancelled`, `store_path_required`, `store_path_missing`, `store_path_not_directory`, `store_register_root_unhealthy`, `store_register_identity_confirmation_required`, `store_register_cancelled`, `store_remote_empty`, `store_remote_requires_hand_edit`, `store_remove_confirmation_required`, `store_remove_cancelled`, `store_remove_path_not_directory`, `store_remove_metadata_missing`, `store_root_missing` (warning in remove, error in doctor), `store_root_not_directory`.
+`store_setup_id_required`, `store_setup_path_required`, `store_setup_path_not_directory`, `store_setup_inside_git_repo`, `store_setup_non_empty_directory`, `store_setup_cancelled`, `store_path_required`, `store_path_missing`, `store_path_not_directory`, `store_root_pointer_declared`, `store_register_root_unhealthy`, `store_register_identity_confirmation_required`, `store_register_cancelled`, `store_remote_empty`, `store_remote_requires_hand_edit`, `store_remove_confirmation_required`, `store_remove_cancelled`, `store_remove_path_not_directory`, `store_remove_metadata_missing`, `store_root_missing` (warning in remove, error in doctor), `store_root_not_directory`.
 
 ### Store git
 `store_git_init_failed`, `store_git_identity_missing`, `store_git_commit_failed`, `store_git_no_commits` (warning), `store_clone_fragile_directories` (warning), `store_remote_divergence` (info, doctor).

docs/cli.md

@@ -215,7 +215,12 @@ openspec store setup team-context --path ~/openspec/team-context --no-init-git -
 
 ### `openspec store register`
 
-Register an existing local store folder.
+Register an existing local store folder. During the stores beta, a root may be
+registered before any changes exist, specs have been applied, or changes have
+been archived; in that case `openspec/changes/`, `openspec/specs/`, and
+`openspec/changes/archive/` may be absent until normal commands create them.
+A config-only repo that declares `store: <id>` remains a pointer to another
+store and is not registered as a store root unless that pointer is removed.
 
 ```bash
 openspec store register [path] [options]

docs/stores-beta/user-guide.md

@@ -308,6 +308,14 @@ tells you which case you're in.
 - **No sync, ever — by design.** OpenSpec never clones, pulls, or pushes.
   A stale checkout shows stale specs until *you* pull; references are
   indexed live from whatever is on disk.
+- **Empty planning folders can be absent.** A new store may not have
+  `openspec/changes/`, `openspec/specs/`, or `openspec/changes/archive/` in Git
+  yet. That is accepted during the beta; those folders appear once normal
+  commands create files for them.
+- **Pointer repos stay pointers.** A config-only repo whose
+  `openspec/config.yaml` declares `store: <id>` is treated as externalized
+  planning, not as a store checkout to register. Remove the `store:` line first
+  if you intentionally want to convert that repo into a local store root.
 - **Some commands stay where they are.** `view`, `templates`, `schemas`,
   and the deprecated noun forms (`openspec change show`, ...) act on the
   current directory only — no `--store`.

src/core/archive.ts

@@ -19,14 +19,24 @@ import {
   type SpecUpdate,
 } from './specs-apply.js';
 
+function isMissingPathError(error: unknown): boolean {
+  return (
+    typeof error === 'object' &&
+    error !== null &&
+    'code' in error &&
+    (error as NodeJS.ErrnoException).code === 'ENOENT'
+  );
+}
+
 async function listActiveChangeNames(changesDir: string): Promise<string[]> {
   try {
     const entries = await fs.readdir(changesDir, { withFileTypes: true });
     return entries
       .filter((entry) => entry.isDirectory() && entry.name !== 'archive')
       .map((entry) => entry.name)
       .sort();
-  } catch {
+  } catch (error) {
+    if (!isMissingPathError(error)) throw error;
     return [];
   }
 }
@@ -192,13 +202,6 @@ export class ArchiveCommand {
     const archiveDir = root.archiveDir;
     const mainSpecsDir = root.specsDir;
 
-    // Check if changes directory exists
-    try {
-      await fs.access(changesDir);
-    } catch {
-      throw new Error("No OpenSpec changes directory found. Run 'openspec init' first.");
-    }
-
     // Get change name interactively if not provided
     if (!changeName) {
       if (json) {
@@ -523,12 +526,7 @@ export class ArchiveCommand {
 
   private async selectChange(changesDir: string): Promise<string | null> {
     const { select } = await import('@inquirer/prompts');
-    // Get all directories in changes (excluding archive)
-    const entries = await fs.readdir(changesDir, { withFileTypes: true });
-    const changeDirs = entries
-      .filter(entry => entry.isDirectory() && entry.name !== 'archive')
-      .map(entry => entry.name)
-      .sort();
+    const changeDirs = await listActiveChangeNames(changesDir);
 
     if (changeDirs.length === 0) {
       console.log('No active changes found.');

src/core/list.ts

@@ -1,7 +1,7 @@
 import { promises as fs } from 'fs';
 import path from 'path';
 import { getTaskProgressForChange, formatTaskStatus } from '../utils/task-progress.js';
-import { readFileSync } from 'fs';
+import { readFileSync, type Dirent } from 'fs';
 import { join } from 'path';
 import { MarkdownParser } from './parsers/markdown-parser.js';
 import type { RootOutput } from './root-selection.js';
@@ -19,6 +19,24 @@ interface ListOptions {
   root?: RootOutput;
 }
 
+function isMissingPathError(error: unknown): boolean {
+  return (
+    typeof error === 'object' &&
+    error !== null &&
+    'code' in error &&
+    (error as NodeJS.ErrnoException).code === 'ENOENT'
+  );
+}
+
+async function readChangeDirectoryEntries(changesDir: string): Promise<Dirent[]> {
+  try {
+    return await fs.readdir(changesDir, { withFileTypes: true });
+  } catch (error) {
+    if (isMissingPathError(error)) return [];
+    throw error;
+  }
+}
+
 /**
  * Get the most recent modification time of any file in a directory (recursive).
  * Falls back to the directory's own mtime if no files are found.
@@ -83,15 +101,8 @@ export class ListCommand {
     if (mode === 'changes') {
       const changesDir = path.join(targetPath, 'openspec', 'changes');
 
-      // Check if changes directory exists
-      try {
-        await fs.access(changesDir);
-      } catch {
-        throw new Error("No OpenSpec changes directory found. Run 'openspec init' first.");
-      }
-
       // Get all directories in changes (excluding archive)
-      const entries = await fs.readdir(changesDir, { withFileTypes: true });
+      const entries = await readChangeDirectoryEntries(changesDir);
       const changeDirs = entries
         .filter(entry => entry.isDirectory() && entry.name !== 'archive')
         .map(entry => entry.name);
@@ -207,4 +218,4 @@ export class ListCommand {
       console.log(`${padding}${padded}     requirements ${spec.requirementCount}`);
     }
   }
-}
+}

src/core/openspec-root.ts

@@ -17,8 +17,8 @@ export const OPENSPEC_ARCHIVE_DIR = 'openspec/changes/archive';
 export const DEFAULT_OPENSPEC_SCHEMA = 'spec-driven';
 export const DIRECTORY_ANCHOR_FILE_NAME = '.gitkeep';
 
-// Git cannot track empty directories, so clones of a fresh store would lose
-// these and fail root-health checks. Anchored at setup time.
+// Git cannot track empty directories, so setup anchors otherwise-empty
+// conventional store directories for teammates who clone the repo later.
 export const ANCHORED_OPENSPEC_DIRS = [OPENSPEC_SPECS_DIR, OPENSPEC_ARCHIVE_DIR] as const;
 
 type PathKind = 'missing' | 'directory' | 'file' | 'other';
@@ -99,6 +99,28 @@ function missingDirectoryDiagnostic(
   return makeStoreDiagnostic('error', code, message, { target });
 }
 
+type OptionalPlanningDirectoryKey = 'specs' | 'changes' | 'archive';
+
+async function inspectOptionalPlanningDirectory(
+  inspection: OpenSpecRootInspection,
+  storeRoot: string,
+  key: OptionalPlanningDirectoryKey,
+  relativePath: string,
+  notDirectoryCode: string,
+  target: string
+): Promise<PathKind> {
+  const kind = await pathKind(path.join(storeRoot, relativePath));
+  inspection[key] = { present: kind === 'directory' };
+  if (kind === 'directory' || kind === 'missing') return kind;
+
+  inspection.diagnostics.push(missingDirectoryDiagnostic(
+    notDirectoryCode,
+    `${relativePath}/ exists but is not a directory.`,
+    target
+  ));
+  return kind;
+}
+
 export async function inspectOpenSpecRoot(storeRoot: string): Promise<OpenSpecRootInspection> {
   const rootKind = await pathKind(storeRoot);
   const inspection = unresolvedInspection();
@@ -166,28 +188,39 @@ export async function inspectOpenSpecRoot(storeRoot: string): Promise<OpenSpecRo
     }
   }
 
-  for (const [key, relativePath, code, message, target] of [
-    ['specs', OPENSPEC_SPECS_DIR, 'openspec_specs_missing', 'Missing openspec/specs/.', 'openspec.specs'],
-    ['changes', OPENSPEC_CHANGES_DIR, 'openspec_changes_missing', 'Missing openspec/changes/.', 'openspec.changes'],
-    ['archive', OPENSPEC_ARCHIVE_DIR, 'openspec_archive_missing', 'Missing openspec/changes/archive/.', 'openspec.archive'],
-  ] as const) {
-    const kind = await pathKind(path.join(storeRoot, relativePath));
-    inspection[key] = { present: kind === 'directory' };
-    if (kind === 'directory') continue;
-
-    inspection.diagnostics.push(missingDirectoryDiagnostic(
-      kind === 'missing' ? code : code.replace('_missing', '_not_directory'),
-      kind === 'missing' ? message : `${relativePath}/ exists but is not a directory.`,
-      target
-    ));
+  await inspectOptionalPlanningDirectory(
+    inspection,
+    storeRoot,
+    'specs',
+    OPENSPEC_SPECS_DIR,
+    'openspec_specs_not_directory',
+    'openspec.specs'
+  );
+  const changesKind = await inspectOptionalPlanningDirectory(
+    inspection,
+    storeRoot,
+    'changes',
+    OPENSPEC_CHANGES_DIR,
+    'openspec_changes_not_directory',
+    'openspec.changes'
+  );
+  if (changesKind === 'directory') {
+    await inspectOptionalPlanningDirectory(
+      inspection,
+      storeRoot,
+      'archive',
+      OPENSPEC_ARCHIVE_DIR,
+      'openspec_archive_not_directory',
+      'openspec.archive'
+    );
+  } else {
+    inspection.archive = { present: false };
   }
 
   inspection.healthy =
     inspection.present === true &&
     inspection.config.present === true &&
-    inspection.specs.present === true &&
-    inspection.changes.present === true &&
-    inspection.archive.present === true;
+    inspection.diagnostics.length === 0;
 
   return inspection;
 }

src/core/store/operations.ts

@@ -5,6 +5,10 @@ import * as path from 'node:path';
 import { promisify } from 'node:util';
 
 import { FileSystemUtils } from '../../utils/file-system.js';
+import {
+  classifyOpenSpecDir,
+  storePointerProblem,
+} from '../project-config.js';
 import {
   ANCHORED_OPENSPEC_DIRS,
   DIRECTORY_ANCHOR_FILE_NAME,
@@ -220,6 +224,33 @@ function alreadyRegisteredDiagnostic(id: string): StoreDiagnostic {
   );
 }
 
+function assertNotConfigOnlyPointerRoot(storeRoot: string): void {
+  const { hasPlanningShape, pointer } = classifyOpenSpecDir(storeRoot);
+  if (hasPlanningShape || pointer.filePath === null) return;
+
+  if (pointer.malformed) {
+    throw new StoreError(
+      `The store declaration in ${pointer.filePath} is invalid (${storePointerProblem(pointer.malformed)}).`,
+      'invalid_store_pointer',
+      {
+        target: 'store.pointer',
+        fix: `Fix or remove the store: line in ${pointer.filePath} before registering this path as a store.`,
+      }
+    );
+  }
+
+  if (pointer.value !== undefined) {
+    throw new StoreError(
+      `This repo's planning is externalized to store '${pointer.value}' (${pointer.filePath}); it is not itself a store root.`,
+      'store_root_pointer_declared',
+      {
+        target: 'store.pointer',
+        fix: 'Register the checkout for the declared store, or remove the store: line first to convert this repo into a local store root.',
+      }
+    );
+  }
+}
+
 function createdPath(relativePath: string, absolutePath: string, kind: CreatedPathLedgerEntry['kind']): CreatedPathLedgerEntry {
   return {
     relativePath,
@@ -459,6 +490,7 @@ async function prepareSetupPlan(
   let backend: StoreGitBackendConfig | undefined;
 
   if (kind === 'directory') {
+    assertNotConfigOnlyPointerRoot(storeRoot);
     metadata = await readStoreMetadataForOperation(storeRoot);
 
     if (metadata) {
@@ -730,6 +762,7 @@ export async function registerExistingStore(
     );
   }
 
+  assertNotConfigOnlyPointerRoot(storeRoot);
   const openspecRoot = await inspectOpenSpecRoot(storeRoot);
   if (!openspecRoot.healthy) {
     const problems =