Align Codex init file strategy

CHANGELOG.md

@@ -7,6 +7,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+### Changed
+
+- **Codex initialization**: `jumbo init`, repair, and `jumbo evolve --yes` now install Codex-managed skills to the documented repository skill location `.agents/skills` while keeping `.codex` limited to Codex hooks/configuration.
+
+### Fixed
+
+- **Codex managed artifact preservation**: Obsolete Jumbo-managed Codex skill copies under `.codex/skills` are removed only when byte-identical to the current managed templates, preserving customized skill content, user files, hook comments, unknown hook settings, and unrelated `.codex` configuration.
+
 ## [3.13.0] - 2026-07-07
 
 ### Removed

docs/getting-started/what-jumbo-creates.md

@@ -69,6 +69,8 @@ These hooks load the session router when an agent session begins and preserve wo
 
 Jumbo copies workflow and maintenance skills from `assets/skills` into the selected agents' skill directories, including bootstrap/session use, lifecycle hooks, command discovery, context maintenance, and correction capture. Additive initialization does not overwrite existing managed skill directories; repair refreshes Jumbo-managed skills from assets while preserving user-created skills.
 
+Codex skills are installed to `.agents/skills`. Jumbo may remove obsolete Codex skill copies from `.codex/skills` during repair or evolve, but only when the obsolete directory is byte-identical to the current managed template and contains no extra user files.
+
 ---
 
 ## How the event store works

docs/reference/commands/maintenance.md

@@ -76,7 +76,7 @@ Runs the complete installation update workflow in sequence:
 7. Refresh managed harness and hook configuration
 8. Rebuild database projections from the event store
 
-The command is designed to be idempotent. Re-running it after a successful evolve should not create duplicate events or duplicate relations. Existing `.jumbo/settings.jsonc` files are upgraded additively: missing defaults are inserted, explicit values and unknown entries are preserved, and invalid JSONC fails instead of being partially rewritten.
+The command is designed to be idempotent. Re-running it after a successful evolve should not create duplicate events or duplicate relations. Existing `.jumbo/settings.jsonc` files are upgraded additively: missing defaults are inserted, explicit values and unknown entries are preserved, and invalid JSONC fails instead of being partially rewritten. Codex skills are refreshed in `.agents/skills`; obsolete Jumbo-managed copies under `.codex/skills` are removed only when they exactly match the current managed templates.
 
 ### Examples
 

docs/reference/commands/project.md

@@ -42,7 +42,7 @@ jumbo project init --non-interactive --name <name> [options]
 4. Always creates bootstrap-only `JUMBO.md` and reference-only `AGENTS.md`
 5. In non-interactive mode, configures all supported agents
 
-Managed agent markdown and JSON hook/settings fragments are loaded from `assets/agent-files`. Managed skills are copied from `assets/skills` to the selected agents' skill directories.
+Managed agent markdown and JSON hook/settings fragments are loaded from `assets/agent-files`. Managed skills are copied from `assets/skills` to the selected agents' skill directories. Codex skills are installed to `.agents/skills`; `.codex` is used for Codex hooks/configuration.
 
 ### Examples
 

docs/reference/project-initialization.md

@@ -87,7 +87,7 @@ Jumbo configures hooks for popular AI coding assistants:
 | Agent | Configuration |
 |-------|---------------|
 | **Claude Code** | `CLAUDE.md`, `.claude/settings.json`, and `.claude/skills` |
-| **Codex** | `.codex/hooks.json` and `.codex/skills` |
+| **Codex** | `.codex/hooks.json` and `.agents/skills` |
 | **GitHub Copilot** | `.github/copilot-instructions.md`, `.github/hooks/hooks.json`, and `.agents/skills` |
 | **Gemini CLI** | `GEMINI.md`, `.gemini/settings.json`, and `.gemini/skills` |
 | **Cursor** | `.cursor/rules/jumbo.mdc` and `.cursor/hooks.json` |
@@ -100,6 +100,8 @@ Managed instruction files are bootstrap-only. `JUMBO.md` tells agents to follow
 
 Jumbo-owned markdown files and JSON hook/settings fragments are loaded from `assets/agent-files`. Managed skills are copied from `assets/skills`, with additive initialization preserving existing user-created skills and repair refreshing Jumbo-managed skill directories.
 
+For Codex, Jumbo uses the repository skill directory `.agents/skills` and keeps `.codex` for documented Codex hooks/configuration. During repair and evolve, obsolete Jumbo-managed skill copies under `.codex/skills` are removed only when they exactly match the current managed templates; customized skills and extra user files are preserved.
+
 ---
 
 ## Update project settings

src/infrastructure/context/project/init/AgentFileProtocol.ts

@@ -42,18 +42,19 @@ const DEFAULT_TEMPLATE_SKILLS_ROOT = path.resolve(
   "assets",
   "skills"
 );
-
 export class AgentFileProtocol implements IAgentFileProtocol {
-  private readonly configurers: IConfigurer[] = [
-    new ClaudeConfigurer(),
-    new GeminiConfigurer(),
-    new CopilotConfigurer(),
-    new VibeConfigurer(),
-    new CodexConfigurer(),
-    new CursorConfigurer(),
-  ];
-
-  constructor(private readonly templateSkillsRoot: string = DEFAULT_TEMPLATE_SKILLS_ROOT) {}
+  private readonly configurers: IConfigurer[];
+
+  constructor(private readonly templateSkillsRoot: string = DEFAULT_TEMPLATE_SKILLS_ROOT) {
+    this.configurers = [
+      new ClaudeConfigurer(),
+      new GeminiConfigurer(),
+      new CopilotConfigurer(),
+      new VibeConfigurer(),
+      new CodexConfigurer(templateSkillsRoot),
+      new CursorConfigurer(),
+    ];
+  }
 
   /**
    * Ensure JUMBO.md exists with full Jumbo instructions