fix: recover Classic roots and parse raw Codex patches

CHANGELOG.md

@@ -2,6 +2,13 @@
 
 All notable changes to @rpamis/comet will be documented in this file.
 
+## What's Changed [0.4.0-beta.16] - 2026-08-05
+
+### Fixed
+
+- **Classic dual-root recovery**: `comet classic root show` and migration dry-runs now remain available when both legacy and docs roots exist, exposing the conflict and a safe remediation path while keeping Classic writes blocked until it is resolved.
+- **Codex Native Hook parsing**: Raw `apply_patch` input now attributes Add, Update, Delete, and standard `+++ b/...` file headers so Native phase protection is applied consistently.
+
 ## What's Changed [0.4.0-beta.15] - 2026-08-05
 
 ### Added

app/commands/doctor.ts

@@ -312,8 +312,7 @@ async function checkClassicLayout(projectPath: string): Promise<CheckResult> {
     return {
       check: 'Classic artifact layout',
       status: 'fail',
-      message:
-        'both openspec/ and docs/openspec/ exist; Classic writes are blocked until the conflict is resolved',
+      message: `both ${path.relative(projectPath, inspection.paths.openSpecRoot).replaceAll('\\', '/')}/ and ${path.relative(projectPath, inspection.alternateRoot).replaceAll('\\', '/')}/ exist; Classic writes are blocked until the conflict is resolved — run comet classic root show, then comet classic root move docs --dry-run to inspect a safe migration; do not delete either root automatically`,
     };
   }
   const configuredRoot = path

assets/manifest.json

@@ -1,5 +1,5 @@
 {
-  "version": "0.4.0-beta.15",
+  "version": "0.4.0-beta.16",
   "skills": [
     "comet/SKILL.md",
     "comet-classic/SKILL.md",

domains/comet-classic/classic-layout.ts

@@ -63,7 +63,7 @@ export class ClassicLayoutConflictError extends Error {
     const configured = classicProjectRelative(projectRoot, configuredRoot);
     const alternate = classicProjectRelative(projectRoot, alternateRoot);
     super(
-      `Classic layout conflict: both ${configured}/ and ${alternate}/ exist; run comet doctor and resolve the conflict before writing`,
+      `Classic layout conflict: both ${configured}/ and ${alternate}/ exist; run comet classic root show, then comet classic root move docs --dry-run to inspect a safe migration before writing`,
     );
     this.name = 'ClassicLayoutConflictError';
   }

domains/comet-classic/classic-root-command.ts

@@ -8,6 +8,7 @@ import {
   assertClassicLayoutReadable,
   classicProjectRelative,
   discoverClassicProject,
+  inspectClassicLayout,
   type ClassicLayoutPaths,
 } from './classic-layout.js';
 import { readWorkflowProjectConfig } from '../workflow-contract/project-config-reader.js';
@@ -177,14 +178,21 @@ export const classicRootCommand: ClassicCommandHandler = async (args) => {
   const [action, target, mode, ...extra] = args;
   if (action === 'show' && target === undefined) {
     const projectRoot = await discoverClassicProject(process.cwd());
-    const layout = await assertClassicLayoutReadable(projectRoot);
+    const layout = await assertClassicLayoutReadable(projectRoot, undefined, {
+      allowAlternateRoot: true,
+    });
+    const inspection = await inspectClassicLayout(projectRoot, layout.artifactLayout);
     return {
       exitCode: 0,
       stdout:
         JSON.stringify({
           schema: 'comet.classic-layout.v1',
           artifactLayout: layout.artifactLayout,
           openSpecRoot: classicProjectRelative(projectRoot, layout.openSpecRoot),
+          alternateRoot: classicProjectRelative(projectRoot, inspection.alternateRoot),
+          configuredRootExists: inspection.configuredRootExists,
+          alternateRootExists: inspection.alternateRootExists,
+          dualRoots: inspection.dualRoots,
           changesRoot: classicProjectRelative(projectRoot, layout.changesDir),
           archiveRoot: classicProjectRelative(projectRoot, layout.archiveDir),
           specsRoot: classicProjectRelative(projectRoot, layout.specsDir),
@@ -201,7 +209,9 @@ export const classicRootCommand: ClassicCommandHandler = async (args) => {
     return usage(language);
   }
 
-  const layout = await assertClassicLayoutReadable(projectRoot);
+  const layout = await assertClassicLayoutReadable(projectRoot, undefined, {
+    allowAlternateRoot: true,
+  });
   const reportMode: RootMoveMode = mode === '--dry-run' ? 'dry-run' : 'complete';
   if (layout.artifactLayout === 'docs') {
     return {

domains/comet-entry/hook-adapter.ts

@@ -145,6 +145,10 @@ export function parseCometHookRequest(source: string, filePath?: string): CometH
   try {
     input = JSON.parse(source) as unknown;
   } catch {
+    const targets = patchTargets(source);
+    if (targets.length > 0) {
+      return { intent: 'write', targets: [...new Set(targets)], toolName: 'apply_patch' };
+    }
     return { intent: 'unknown', targets: [], toolName: null };
   }
   if (!isRecord(input)) return { intent: 'unknown', targets: [], toolName: null };

package.json

@@ -1,6 +1,6 @@
 {
   "name": "@rpamis/comet",
-  "version": "0.4.0-beta.15",
+  "version": "0.4.0-beta.16",
   "description": "Agent Skill Harness For Turning Ideas Into Evaluated Workflows",
   "keywords": [
     "comet",

test/app/cli-help.test.ts

@@ -29,7 +29,7 @@ describe('CLI help text', () => {
     expect(help.status, help.stderr).toBe(0);
     expect(help.stdout).toContain(tagline);
     expect(packageJson.description).toBe(tagline);
-    expect(packageJson.version).toBe('0.4.0-beta.15');
+    expect(packageJson.version).toBe('0.4.0-beta.16');
   });
 
   it('marks bundle as the advanced backend and skill Engine runs as advanced', () => {

test/app/doctor.test.ts

@@ -1108,9 +1108,12 @@ describe('doctor command', () => {
       status: string;
       message: string;
     }>;
-    expect(results.find((result) => result.check === 'Classic artifact layout')).toMatchObject({
-      status: 'fail',
-    });
+    const layoutResult = results.find((result) => result.check === 'Classic artifact layout');
+    expect(layoutResult).toMatchObject({ status: 'fail' });
+    expect(layoutResult?.message).toContain('openspec/');
+    expect(layoutResult?.message).toContain('docs/openspec/');
+    expect(layoutResult?.message).toContain('comet classic root show');
+    expect(layoutResult?.message).toContain('comet classic root move docs --dry-run');
     const stateResult = results.find((result) => result.check === '.comet.yaml: current-state');
     expect(stateResult).toMatchObject({
       status: 'pass',

test/domains/comet-classic/classic-root-command.test.ts

@@ -80,14 +80,47 @@ describe('Classic root show', () => {
     expect(result.stderr).toContain('Configured Classic OpenSpec root is missing');
   });
 
-  it('fails when both roots exist', async () => {
+  it('reports both roots without blocking read-only root inspection', async () => {
     await fs.mkdir(path.join(projectRoot, 'openspec'), { recursive: true });
     await fs.mkdir(path.join(projectRoot, 'docs', 'openspec'), { recursive: true });
 
     const result = await runClassicCli(['root', 'show']);
 
-    expect(result.exitCode).not.toBe(0);
-    expect(result.stderr).toContain('Classic layout conflict');
+    expect(result.exitCode).toBe(0);
+    expect(JSON.parse(result.stdout ?? '{}')).toMatchObject({
+      artifactLayout: 'legacy',
+      openSpecRoot: 'openspec',
+      alternateRoot: 'docs/openspec',
+      configuredRootExists: true,
+      alternateRootExists: true,
+      dualRoots: true,
+    });
+  });
+
+  it('exposes a safe dry-run path when both roots exist', async () => {
+    await fs.mkdir(path.join(projectRoot, 'openspec', 'changes', 'legacy'), {
+      recursive: true,
+    });
+    await fs.mkdir(path.join(projectRoot, 'docs', 'openspec', 'changes', 'docs'), {
+      recursive: true,
+    });
+
+    const result = await runClassicCli(['root', 'move', 'docs', '--dry-run']);
+
+    expect(result.exitCode).toBe(0);
+    expect(result.stdout).toContain('目标初始状态: 非空目录');
+    expect(result.stdout).toContain('冲突:');
+    expect(result.stdout).toContain('docs 目标目录非空');
+    expect(result.stdout).toContain('请先解决上述冲突或阻塞项');
+
+    const configBefore = await fs.readFile(path.join(projectRoot, '.comet', 'config.yaml'), 'utf8');
+    const apply = await runClassicCli(['root', 'move', 'docs', '--apply']);
+
+    expect(apply.exitCode).toBe(70);
+    expect(apply.stderr).toContain('Classic 根目录迁移失败');
+    expect(await fs.readFile(path.join(projectRoot, '.comet', 'config.yaml'), 'utf8')).toBe(
+      configBefore,
+    );
   });
 
   it('fails when a managed root is a directory link', async () => {

test/domains/comet-entry/hook-adapter.test.ts

@@ -81,6 +81,32 @@ describe('Comet Hook platform adapter', () => {
     ).toEqual({ intent: 'write', targets: ['src/b.ts'], toolName: 'apply_patch' });
   });
 
+  it('normalizes raw Codex apply_patch input from Hook stdin', () => {
+    const patch = [
+      '*** Begin Patch',
+      '*** Update File: src/existing.ts',
+      '*** Add File: src/new.ts',
+      '*** Delete File: src/old.ts',
+      '*** End Patch',
+    ].join('\n');
+
+    expect(parseCometHookRequest(patch)).toEqual({
+      intent: 'write',
+      targets: ['src/existing.ts', 'src/new.ts', 'src/old.ts'],
+      toolName: 'apply_patch',
+    });
+  });
+
+  it('normalizes standard unified-diff headers from raw patch input', () => {
+    const patch = ['--- a/src/old.ts', '+++ b/src/new.ts'].join('\n');
+
+    expect(parseCometHookRequest(patch)).toEqual({
+      intent: 'write',
+      targets: ['src/new.ts'],
+      toolName: 'apply_patch',
+    });
+  });
+
   it('keeps an absolute Hook working directory for linked-worktree routing', () => {
     const cwd = path.resolve('linked-worktree');
     expect(

test/domains/comet-entry/hook-router-runtime.test.ts

@@ -102,4 +102,26 @@ describe('packaged Hook Router worktree isolation', () => {
     expect(primaryRequest.status).toBe(2);
     expect(primaryRequest.stderr).toContain('primary-shape');
   });
+
+  it('enforces Native Shape for raw Codex apply_patch input', async () => {
+    await configureChange(primary, 'raw-patch-shape', 'shape');
+    const patch = [
+      '*** Begin Patch',
+      '*** Update File: src/app.ts',
+      '@@',
+      '-old',
+      '+new',
+      '*** End Patch',
+    ].join('\n');
+
+    const result = spawnSync(
+      process.execPath,
+      [router, '--platform', 'codex', '--project-root', primary],
+      { cwd: primary, input: patch, encoding: 'utf8', timeout: 20_000 },
+    );
+
+    expect(result.status, result.stderr).toBe(2);
+    expect(result.stderr).toContain('raw-patch-shape');
+    expect(result.stderr).toContain('only allowed in build');
+  });
 });

test/domains/comet-entry/project-status.test.ts

@@ -302,6 +302,8 @@ describe('Comet project status', () => {
       changes: [],
       error: expect.stringContaining('Classic layout conflict'),
     });
+    expect(status.workflows.classic.error).toContain('comet classic root show');
+    expect(status.workflows.classic.error).toContain('comet classic root move docs --dry-run');
     expect(status.unmanagedOpenSpec).toEqual([]);
   });
 

test/repository/release-metadata.test.ts

@@ -16,7 +16,7 @@ describe('release metadata', () => {
       readFileSync(path.join(repositoryRoot, 'assets', 'manifest.json'), 'utf8'),
     ) as { version: string };
 
-    expect(packageJson.version).toBe('0.4.0-beta.15');
+    expect(packageJson.version).toBe('0.4.0-beta.16');
     expect(packageLock.version).toBe(packageJson.version);
     expect(packageLock.packages[''].version).toBe(packageJson.version);
     expect(assetsManifest.version).toBe(packageJson.version);