fix: recover Classic roots and parse raw Codex patches (#283)

* fix: recover Classic roots and parse raw Codex patches

* fix(classic): allow standalone OpenSpec root coexistence

* fix(classic): enforce valid layout evidence boundaries

* fix(security): update vulnerable dependencies

* fix(test): align standalone OpenSpec layout expectation

Author: benym

CHANGELOG.md

@@ -2,6 +2,17 @@
 
 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/OpenSpec coexistence**: Classic now uses only the configured artifact root, so a standalone OpenSpec project can keep the other root at the same time; explicit root migration still refuses to overwrite a non-empty destination.
+- **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.
+
+### Security
+
+- **Dependency security updates**: Updated PostCSS, Undici, and brace-expansion to patched releases to address reported dependency vulnerabilities.
+
 ## What's Changed [0.4.0-beta.15] - 2026-08-05
 
 ### Added

app/commands/doctor.ts

@@ -309,11 +309,16 @@ async function checkClassicLayout(projectPath: string): Promise<CheckResult> {
     };
   }
   if (inspection.dualRoots) {
+    const configuredRoot = path
+      .relative(projectPath, inspection.paths.openSpecRoot)
+      .replaceAll('\\', '/');
+    const alternateRoot = path
+      .relative(projectPath, inspection.alternateRoot)
+      .replaceAll('\\', '/');
     return {
       check: 'Classic artifact layout',
-      status: 'fail',
-      message:
-        'both openspec/ and docs/openspec/ exist; Classic writes are blocked until the conflict is resolved',
+      status: 'pass',
+      message: `${inspection.paths.artifactLayout}: configured ${configuredRoot}/ present; standalone OpenSpec root ${alternateRoot}/ also present and ignored by Comet`,
     };
   }
   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",