oh-my-customcodex 0.3.7 → 0.3.9

package/README.md

@@ -29,7 +29,8 @@ oh-my-customcodex is built on two ideas:
 
 | Compile Concept | oh-my-customcodex |
 |----------------|-----------------|
-| Source code | `.agents/skills/` — reusable knowledge and workflows |
+| Source repository authoring | `.codex/skills/` — skill definitions maintained by this package itself |
+| Installed runtime skills | `.agents/skills/` — reusable knowledge and workflows deployed into managed projects |
 | Build artifacts | `.codex/agents/` — executable specialists assembled from skills |
 | Compiler | `mgr-sauron` (R017) — structural verification and integrity |
 | Spec | `.codex/rules/` — constraints and build rules |
@@ -270,21 +271,33 @@ omcustomcodex serve-stop            # Stop Web UI
 
 ## Project Structure
 
+### Managed project runtime
+
 ```
 your-project/
 ├── AGENTS.md                   # Entry point
 ├── .codex/
 │   ├── agents/                 # 48 agent definitions
-│   ├── skills/                 # 112 skill modules
 │   ├── rules/                  # 22 governance rules (R000-R021)
 │   ├── hooks/                  # 15 lifecycle hook scripts
 │   ├── schemas/                # Tool input validation schemas
 │   ├── specs/                  # Extracted canonical specs
 │   ├── contexts/               # 4 shared context files
 │   └── ontology/               # Knowledge graph for RAG
+├── .agents/
+│   └── skills/                 # 112 installed skill modules
 └── guides/                     # 40 reference documents
 ```
 
+### Source Repository And Compatibility Surfaces
+
+- This repository keeps package-authoring skills in `.codex/skills/`; that is a source-repo surface, not the installed project skill path.
+- Installed projects use `.agents/skills/` for managed skills and `.codex/agents/*.md` for managed agents.
+- `templates/.claude/` and `templates/CLAUDE.md*` remain upstream-compatible template inputs; they are not the active Codex runtime surface after install.
+- `.codex/hooks/` is the OMX-managed hook script layer used by this package. Native Codex `hooks.json` discovery is a separate contract and is not generated by `omcustomcodex` today.
+- Native Codex custom subagents in `.codex/agents/*.toml` may coexist, but `omcustomcodex` currently manages `.codex/agents/*.md` as its own agent contract.
+- Project-scoped MCP configuration lives in `.codex/config.toml`, and the managed project registry lives in `~/.oh-my-customcodex/projects.json`.
+
 ---
 
 ## External Tool Integrations

package/dist/cli/index.js

@@ -3091,7 +3091,7 @@ var init_package = __esm(() => {
     workspaces: [
       "packages/*"
     ],
-    version: "0.3.7",
+    version: "0.3.9",
     description: "Batteries-included agent harness on top of GPT Codex + OMX",
     type: "module",
     bin: {
@@ -26742,7 +26742,7 @@ function installCodex(deps = defaultDeps) {
     if (os === "darwin") {
       try {
         info("codex.installing_brew");
-        deps.exec("brew install openai-codex", {
+        deps.exec("brew install --cask codex", {
           stdio: "inherit",
           timeout: 120000
         });
@@ -28614,11 +28614,28 @@ init_fs();
 init_logger();
 init_layout();
 import { execSync as execSync6 } from "node:child_process";
-import { writeFile as writeFile2 } from "node:fs/promises";
+import { readFile as readFile3, writeFile as writeFile2 } from "node:fs/promises";
 import { join as join8 } from "node:path";
+var PROJECT_CONFIG_DIR = ".codex";
+var PROJECT_CONFIG_FILE = "config.toml";
+var ONTOLOGY_SERVER_TABLE = "[mcp_servers.ontology-rag]";
+function getProjectMCPConfigPath(targetDir) {
+  return join8(targetDir, PROJECT_CONFIG_DIR, PROJECT_CONFIG_FILE);
+}
+function renderOntologyMCPBlock(ontologyDir) {
+  return `${ONTOLOGY_SERVER_TABLE}
+command = ".venv/bin/python"
+args = ["-m", "ontology_rag.mcp_server"]
+
+[mcp_servers.ontology-rag.env]
+ONTOLOGY_DIR = "${ontologyDir}"
+`;
+}
+function hasOntologyMCPConfig(content) {
+  return content.includes(ONTOLOGY_SERVER_TABLE);
+}
 async function generateMCPConfig(targetDir) {
   const layout = getProviderLayout();
-  const mcpConfigPath = join8(targetDir, ".mcp.json");
   const ontologyDir = join8(layout.rootDir, "ontology");
   const ontologyExists = await fileExists(join8(targetDir, ontologyDir));
   if (!ontologyExists) {
@@ -28628,7 +28645,7 @@ async function generateMCPConfig(targetDir) {
     execSync6("uv --version", { stdio: "pipe" });
   } catch {
     warn("uv (Python package manager) not found. Install it with: curl -LsSf https://astral.sh/uv/install.sh | sh");
-    warn("Skipping ontology-rag MCP configuration. You can set it up manually later.");
+    warn("Skipping ontology-rag MCP configuration in .codex/config.toml. You can set it up manually later.");
     return;
   }
   try {
@@ -28637,41 +28654,24 @@ async function generateMCPConfig(targetDir) {
   } catch (error2) {
     const msg = error2 instanceof Error ? error2.message : String(error2);
     warn(`Failed to setup ontology-rag: ${msg}`);
-    warn("You can configure the MCP server manually. See: https://github.com/baekenough/oh-my-customcodex/tree/develop/packages/ontology-rag");
+    warn("You can configure the MCP server manually in .codex/config.toml. See: https://github.com/baekenough/oh-my-customcodex/tree/develop/packages/ontology-rag");
     return;
   }
-  const config = {
-    mcpServers: {
-      "ontology-rag": {
-        type: "stdio",
-        command: ".venv/bin/python",
-        args: ["-m", "ontology_rag.mcp_server"],
-        env: {
-          ONTOLOGY_DIR: ontologyDir
-        }
-      }
-    }
-  };
-  const existingConfigPath = mcpConfigPath;
-  if (await fileExists(existingConfigPath)) {
-    try {
-      const { readFile: readFile3 } = await import("node:fs/promises");
-      const existingContent = await readFile3(existingConfigPath, "utf-8");
-      const existing = JSON.parse(existingContent);
-      if (!existing.mcpServers?.["ontology-rag"]) {
-        existing.mcpServers = existing.mcpServers || {};
-        existing.mcpServers["ontology-rag"] = config.mcpServers["ontology-rag"];
-        await writeFile2(mcpConfigPath, `${JSON.stringify(existing, null, 2)}
-`);
-      }
-    } catch {
-      await writeFile2(mcpConfigPath, `${JSON.stringify(config, null, 2)}
-`);
+  const configPath = getProjectMCPConfigPath(targetDir);
+  await ensureDirectory(join8(targetDir, PROJECT_CONFIG_DIR));
+  let existingContent = "";
+  if (await fileExists(configPath)) {
+    existingContent = await readFile3(configPath, "utf-8");
+    if (hasOntologyMCPConfig(existingContent)) {
+      info("ontology-rag MCP server already configured");
+      return;
     }
-  } else {
-    await writeFile2(mcpConfigPath, `${JSON.stringify(config, null, 2)}
-`);
   }
+  const block = renderOntologyMCPBlock(ontologyDir);
+  const nextContent = existingContent.trim() ? `${existingContent.trimEnd()}
+
+${block}` : block;
+  await writeFile2(configPath, nextContent, "utf-8");
   info("ontology-rag MCP server configured successfully");
 }
 async function checkUvAvailable() {
@@ -30689,7 +30689,7 @@ import { join as join14 } from "node:path";
 // src/cli/serve.ts
 import { spawn } from "node:child_process";
 import { existsSync as existsSync3 } from "node:fs";
-import { readFile as readFile3, unlink, writeFile as writeFile3 } from "node:fs/promises";
+import { readFile as readFile4, unlink, writeFile as writeFile3 } from "node:fs/promises";
 import { join as join13 } from "node:path";
 var DEFAULT_PORT = 4321;
 var PID_FILE = join13(process.env.HOME ?? "~", ".omcodex-serve.pid");
@@ -30709,7 +30709,7 @@ function buildServeEnv(port, projectRoot) {
 async function readPidFromKnownFiles() {
   for (const pidFile of [PID_FILE, LEGACY_PID_FILE]) {
     try {
-      const raw = await readFile3(pidFile, "utf-8");
+      const raw = await readFile4(pidFile, "utf-8");
       const pid = Number(raw.trim());
       if (Number.isFinite(pid) && pid > 0) {
         return { pid, path: pidFile };

package/dist/index.js

@@ -1381,7 +1381,7 @@ function installCodex(deps = defaultDeps) {
     if (os === "darwin") {
       try {
         info("codex.installing_brew");
-        deps.exec("brew install openai-codex", {
+        deps.exec("brew install --cask codex", {
           stdio: "inherit",
           timeout: 120000
         });
@@ -2180,7 +2180,7 @@ var package_default = {
   workspaces: [
     "packages/*"
   ],
-  version: "0.3.7",
+  version: "0.3.9",
   description: "Batteries-included agent harness on top of GPT Codex + OMX",
   type: "module",
   bin: {

package/package.json

@@ -3,7 +3,7 @@
   "workspaces": [
     "packages/*"
   ],
-  "version": "0.3.7",
+  "version": "0.3.9",
   "description": "Batteries-included agent harness on top of GPT Codex + OMX",
   "type": "module",
   "bin": {

package/templates/.claude/rules/MUST-agent-design.md

@@ -232,7 +232,7 @@ Skills persist output to `.codex/outputs/sessions/{YYYY-MM-DD}/{skill-name}-{HHm
 
 <!-- DETAIL: Artifact Output full spec
 **Format**: Metadata header with `skill`, `date`, `query` fields, followed by skill output content.
-**Rules**: Opt-in per skill, final subagent writes (R010 compliance), Skills create directory (mkdir -p), .codex/outputs/ is git-untracked, no indexing required.
+**Rules**: Opt-in per skill, final subagent writes with a file-write API that creates missing parent directories (R010 compliance), do not pre-create session output directories with Bash, .codex/outputs/ is git-untracked, no indexing required.
 -->
 
 ## Separation of Concerns

package/templates/.claude/skills/dev-review/SKILL.md

@@ -122,7 +122,7 @@ If only PASS/INFO: proceed automatically.
    query: "{original user query}"
    ---
    ```
-   The review agent creates the directory and writes the artifact before returning results (R010 compliance).
+   The review agent writes the artifact file before returning results; use a file-write API that creates missing parent directories instead of any Bash directory-creation pre-step (R010 compliance).
 
 ## Agent Selection
 

package/templates/.claude/skills/research/SKILL.md

@@ -213,7 +213,7 @@ Convergence expected by round 3. Hard stop at round 30.
    query: "{original user query}"
    ---
    ```
-   The agent creates the directory (`mkdir -p`) before writing. This is a subagent operation (R010 compliance).
+   The agent writes the artifact file using a file-write API that creates missing parent directories; do not run any Bash directory-creation pre-step for session outputs (R010 compliance).
 3. GitHub issue auto-created with findings
 4. Action items with effort estimates
 

package/templates/AGENTS.md.en

@@ -129,10 +129,11 @@ project/
 +-- AGENTS.md                    # Entry point
 +-- .codex/
 |   +-- agents/                  # Subagent definitions (44 files)
-|   +-- skills/                  # Skills (74 directories)
 |   +-- rules/                   # Global rules (R000-R020)
 |   +-- hooks/                   # Hook scripts (security, validation, HUD)
 |   +-- contexts/                # Context files (ecomode)
++-- .agents/
+|   +-- skills/                  # Installed skills (74 directories)
 +-- guides/                      # Reference docs (26 topics)
 ```
 

package/templates/AGENTS.md.ko

@@ -129,10 +129,11 @@ project/
 +-- AGENTS.md                    # 진입점
 +-- .codex/
 |   +-- agents/                  # 서브에이전트 정의 (44 파일)
-|   +-- skills/                  # 스킬 (74 디렉토리)
 |   +-- rules/                   # 전역 규칙 (R000-R020)
 |   +-- hooks/                   # 훅 스크립트 (보안, 검증, HUD)
 |   +-- contexts/                # 컨텍스트 파일 (ecomode)
++-- .agents/
+|   +-- skills/                  # 설치된 스킬 (74 디렉토리)
 +-- guides/                      # 레퍼런스 문서 (26 토픽)
 ```
 

package/templates/guides/agents-md-quality/README.md

@@ -2,7 +2,7 @@
 
 ## Overview
 
-Quality criteria for `.claude/agents/*.md` files. Adapted from ETH Zurich research on LLM-generated agent configurations, modified to fit oh-my-customcodex's "create, connect, use" philosophy.
+Quality criteria for managed agent markdown files (the `omcustomcodex` runtime contract uses `.codex/agents/*.md`). Adapted from ETH Zurich research on LLM-generated agent configurations, modified to fit oh-my-customcodex's "create, connect, use" philosophy.
 
 ## Core Principle: LLM Generation + Human Verification
 

package/templates/manifest.json

@@ -1,6 +1,6 @@
 {
-  "version": "0.3.7",
-  "lastUpdated": "2026-04-22T05:10:00.000Z",
+  "version": "0.3.9",
+  "lastUpdated": "2026-04-24T08:45:48.000Z",
   "components": [
     {
       "name": "rules",