feat: migrate Codex/agy init to native skills workflow (#1906)

* feat: migrate codex and agy to native skills flow

* fix: harden codex skill frontmatter and script fallback

* fix: clarify skills separator default expansion

* fix: rewrite agent_scripts paths for codex skills

* fix: align kimi guidance and platform-aware codex fallback

.github/workflows/scripts/create-release-packages.ps1

@@ -201,20 +201,22 @@ agent: $basename
     }
 }
 
-# Create Kimi Code skills in .kimi/skills/<name>/SKILL.md format.
-# Kimi CLI discovers skills as directories containing a SKILL.md file,
-# invoked with /skill:<name> (e.g. /skill:speckit.specify).
-function New-KimiSkills {
+# Create skills in <skills_dir>\<name>\SKILL.md format.
+# Most agents use hyphenated names (e.g. speckit-plan); Kimi is the
+# current dotted-name exception (e.g. speckit.plan).
+function New-Skills {
     param(
         [string]$SkillsDir,
-        [string]$ScriptVariant
+        [string]$ScriptVariant,
+        [string]$AgentName,
+        [string]$Separator = '-'
     )
 
     $templates = Get-ChildItem -Path "templates/commands/*.md" -File -ErrorAction SilentlyContinue
 
     foreach ($template in $templates) {
         $name = [System.IO.Path]::GetFileNameWithoutExtension($template.Name)
-        $skillName = "speckit.$name"
+        $skillName = "speckit${Separator}$name"
         $skillDir = Join-Path $SkillsDir $skillName
         New-Item -ItemType Directory -Force -Path $skillDir | Out-Null
 
@@ -267,7 +269,7 @@ function New-KimiSkills {
 
         $body = $outputLines -join "`n"
         $body = $body -replace '\{ARGS\}', '$ARGUMENTS'
-        $body = $body -replace '__AGENT__', 'kimi'
+        $body = $body -replace '__AGENT__', $AgentName
         $body = Rewrite-Paths -Content $body
 
         # Strip existing frontmatter, keep only body
@@ -396,8 +398,9 @@ function Build-Variant {
             Generate-Commands -Agent 'windsurf' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
         }
         'codex' {
-            $cmdDir = Join-Path $baseDir ".codex/prompts"
-            Generate-Commands -Agent 'codex' -Extension 'md' -ArgFormat '$ARGUMENTS' -OutputDir $cmdDir -ScriptVariant $Script
+            $skillsDir = Join-Path $baseDir ".agents/skills"
+            New-Item -ItemType Directory -Force -Path $skillsDir | Out-Null
+            New-Skills -SkillsDir $skillsDir -ScriptVariant $Script -AgentName 'codex' -Separator '-'
         }
         'kilocode' {
             $cmdDir = Join-Path $baseDir ".kilocode/workflows"
@@ -452,7 +455,7 @@ function Build-Variant {
         'kimi' {
             $skillsDir = Join-Path $baseDir ".kimi/skills"
             New-Item -ItemType Directory -Force -Path $skillsDir | Out-Null
-            New-KimiSkills -SkillsDir $skillsDir -ScriptVariant $Script
+            New-Skills -SkillsDir $skillsDir -ScriptVariant $Script -AgentName 'kimi' -Separator '.'
         }
         'trae' {
             $rulesDir = Join-Path $baseDir ".trae/rules"

.github/workflows/scripts/create-release-packages.sh

@@ -121,18 +121,20 @@ EOF
   done
 }
 
-# Create Kimi Code skills in .kimi/skills/<name>/SKILL.md format.
-# Kimi CLI discovers skills as directories containing a SKILL.md file,
-# invoked with /skill:<name> (e.g. /skill:speckit.specify).
-create_kimi_skills() {
+# Create skills in <skills_dir>/<name>/SKILL.md format.
+# Most agents use hyphenated names (e.g. speckit-plan); Kimi is the
+# current dotted-name exception (e.g. speckit.plan).
+create_skills() {
   local skills_dir="$1"
   local script_variant="$2"
+  local agent_name="$3"
+  local separator="${4:-"-"}"
 
   for template in templates/commands/*.md; do
     [[ -f "$template" ]] || continue
     local name
     name=$(basename "$template" .md)
-    local skill_name="speckit.${name}"
+    local skill_name="speckit${separator}${name}"
     local skill_dir="${skills_dir}/${skill_name}"
     mkdir -p "$skill_dir"
 
@@ -175,9 +177,9 @@ create_kimi_skills() {
       in_frontmatter && skip_scripts && /^[[:space:]]/ { next }
       { print }
     ')
-    body=$(printf '%s\n' "$body" | sed 's/{ARGS}/\$ARGUMENTS/g' | sed 's/__AGENT__/kimi/g' | rewrite_paths)
+    body=$(printf '%s\n' "$body" | sed 's/{ARGS}/\$ARGUMENTS/g' | sed "s/__AGENT__/$agent_name/g" | rewrite_paths)
 
-    # Strip existing frontmatter and prepend Kimi frontmatter
+    # Strip existing frontmatter and prepend skills frontmatter.
     local template_body
     template_body=$(printf '%s\n' "$body" | awk '/^---/{p++; if(p==2){found=1; next}} found')
 
@@ -249,8 +251,8 @@ build_variant() {
       mkdir -p "$base_dir/.windsurf/workflows"
       generate_commands windsurf md "\$ARGUMENTS" "$base_dir/.windsurf/workflows" "$script" ;;
     codex)
-      mkdir -p "$base_dir/.codex/prompts"
-      generate_commands codex md "\$ARGUMENTS" "$base_dir/.codex/prompts" "$script" ;;
+      mkdir -p "$base_dir/.agents/skills"
+      create_skills "$base_dir/.agents/skills" "$script" "codex" "-" ;;
     kilocode)
       mkdir -p "$base_dir/.kilocode/workflows"
       generate_commands kilocode md "\$ARGUMENTS" "$base_dir/.kilocode/workflows" "$script" ;;
@@ -290,7 +292,7 @@ build_variant() {
       generate_commands vibe md "\$ARGUMENTS" "$base_dir/.vibe/prompts" "$script" ;;
     kimi)
       mkdir -p "$base_dir/.kimi/skills"
-      create_kimi_skills "$base_dir/.kimi/skills" "$script" ;;
+      create_skills "$base_dir/.kimi/skills" "$script" "kimi" "." ;;
     trae)
       mkdir -p "$base_dir/.trae/rules"
       generate_commands trae md "\$ARGUMENTS" "$base_dir/.trae/rules" "$script" ;;

README.md

@@ -99,7 +99,7 @@ uvx --from git+https://github.com/github/spec-kit.git specify init --here --ai c
 
 ### 2. Establish project principles
 
-Launch your AI assistant in the project directory. The `/speckit.*` commands are available in the assistant.
+Launch your AI assistant in the project directory. Most agents expose spec-kit as `/speckit.*` slash commands; Codex CLI in skills mode uses `$speckit-*` instead.
 
 Use the **`/speckit.constitution`** command to create your project's governing principles and development guidelines that will guide all subsequent development.
 
@@ -173,7 +173,7 @@ See Spec-Driven Development in action across different scenarios with these comm
 | [Auggie CLI](https://docs.augmentcode.com/cli/overview)                              | ✅      |                                                                                                                                           |
 | [Claude Code](https://www.anthropic.com/claude-code)                                 | ✅      |                                                                                                                                           |
 | [CodeBuddy CLI](https://www.codebuddy.ai/cli)                                        | ✅      |                                                                                                                                           |
-| [Codex CLI](https://github.com/openai/codex)                                         | ✅      |                                                                                                                                           |
+| [Codex CLI](https://github.com/openai/codex)                                         | ✅      | Requires `--ai-skills`. Codex recommends [skills](https://developers.openai.com/codex/skills) and treats [custom prompts](https://developers.openai.com/codex/custom-prompts) as deprecated. Spec-kit installs Codex skills into `.agents/skills` and invokes them as `$speckit-<command>`. |
 | [Cursor](https://cursor.sh/)                                                         | ✅      |                                                                                                                                           |
 | [Gemini CLI](https://github.com/google-gemini/gemini-cli)                            | ✅      |                                                                                                                                           |
 | [GitHub Copilot](https://code.visualstudio.com/)                                     | ✅      |                                                                                                                                           |
@@ -258,6 +258,9 @@ specify init my-project --ai bob
 # Initialize with Pi Coding Agent support
 specify init my-project --ai pi
 
+# Initialize with Codex CLI support
+specify init my-project --ai codex --ai-skills
+
 # Initialize with Antigravity support
 specify init my-project --ai agy --ai-skills
 
@@ -298,7 +301,9 @@ specify check
 
 ### Available Slash Commands
 
-After running `specify init`, your AI coding agent will have access to these slash commands for structured development:
+After running `specify init`, your AI coding agent will have access to these slash commands for structured development.
+
+For Codex CLI, `--ai-skills` installs spec-kit as agent skills instead of slash-command prompt files. In Codex skills mode, invoke spec-kit as `$speckit-constitution`, `$speckit-specify`, `$speckit-plan`, `$speckit-tasks`, and `$speckit-implement`.
 
 #### Core Commands
 
@@ -484,11 +489,11 @@ specify init <project_name> --ai copilot
 
 # Or in current directory:
 specify init . --ai claude
-specify init . --ai codex
+specify init . --ai codex --ai-skills
 
 # or use --here flag
 specify init --here --ai claude
-specify init --here --ai codex
+specify init --here --ai codex --ai-skills
 
 # Force merge into a non-empty current directory
 specify init . --force --ai claude

src/specify_cli/__init__.py

@@ -31,7 +31,6 @@ import sys
 import zipfile
 import tempfile
 import shutil
-import shlex
 import json
 import json5
 import stat
@@ -172,8 +171,8 @@ AGENT_CONFIG = {
     },
     "codex": {
         "name": "Codex CLI",
-        "folder": ".codex/",
-        "commands_subdir": "prompts",  # Special: uses prompts/ not commands/
+        "folder": ".agents/",
+        "commands_subdir": "skills",  # Codex now uses project skills directly
         "install_url": "https://github.com/openai/codex",
         "requires_cli": True,
     },
@@ -1211,6 +1210,9 @@ AGENT_SKILLS_DIR_OVERRIDES = {
 # Default skills directory for agents not in AGENT_CONFIG
 DEFAULT_SKILLS_DIR = ".agents/skills"
 
+# Agents whose downloaded template already contains skills in the final layout.
+NATIVE_SKILLS_AGENTS = {"codex", "kimi"}
+
 # Enhanced descriptions for each spec-kit command skill
 SKILL_DESCRIPTIONS = {
     "specify": "Create or update feature specifications from natural language descriptions. Use when starting new features or refining requirements. Generates spec.md with user stories, functional requirements, and acceptance criteria following spec-driven development methodology.",
@@ -1339,8 +1341,6 @@ def install_ai_skills(project_path: Path, selected_ai: str, tracker: StepTracker
                 command_name = command_name[len("speckit."):]
             if command_name.endswith(".agent"):
                 command_name = command_name[:-len(".agent")]
-            # Kimi CLI discovers skills by directory name and invokes them as
-            # /skill:<name> — use dot separator to match packaging convention.
             if selected_ai == "kimi":
                 skill_name = f"speckit.{command_name}"
             else:
@@ -1416,20 +1416,45 @@ def install_ai_skills(project_path: Path, selected_ai: str, tracker: StepTracker
     return installed_count > 0 or skipped_count > 0
 
 
-def _handle_agy_deprecation(console: Console) -> None:
-    """
-    Print the deprecation error for the Antigravity (agy) agent and exit.
+def _has_bundled_skills(project_path: Path, selected_ai: str) -> bool:
+    """Return True when a native-skills agent has spec-kit bundled skills."""
+    skills_dir = _get_skills_dir(project_path, selected_ai)
+    if not skills_dir.is_dir():
+        return False
 
-    Context for future AI reviewers (e.g., GitHub Copilot):
-    - Prior to Antigravity v1.20.5, users could rely on explicit agent command definitions generated by this tool.
-    - v1.20.5 removed this "command support" in favor of "Agent Skills".
-    - `specify_cli` handles this by throwing a fail-fast deprecation error if `--ai agy` is 
-      invoked without the accompanying `--ai-skills` flag. Users are instructed to add 
-      the skills flag to generate agent skills templates instead.
-    """
-    console.print("\n[red]Error:[/red] Explicit command support was deprecated in Antigravity version 1.20.5.")
+    pattern = "speckit.*/SKILL.md" if selected_ai == "kimi" else "speckit-*/SKILL.md"
+    return any(skills_dir.glob(pattern))
+
+
+AGENT_SKILLS_MIGRATIONS = {
+    "agy": {
+        "error": "Explicit command support was deprecated in Antigravity version 1.20.5.",
+        "usage": "specify init <project> --ai agy --ai-skills",
+        "interactive_note": (
+            "'agy' was selected interactively; enabling [cyan]--ai-skills[/cyan] "
+            "automatically for compatibility (explicit .agent/commands usage is deprecated)."
+        ),
+    },
+    "codex": {
+        "error": (
+            "Custom prompt-based spec-kit initialization is deprecated for Codex CLI; "
+            "use agent skills instead."
+        ),
+        "usage": "specify init <project> --ai codex --ai-skills",
+        "interactive_note": (
+            "'codex' was selected interactively; enabling [cyan]--ai-skills[/cyan] "
+            "automatically for compatibility (.agents/skills is the recommended Codex layout)."
+        ),
+    },
+}
+
+
+def _handle_agent_skills_migration(console: Console, agent_key: str) -> None:
+    """Print a fail-fast migration error for agents that now require skills."""
+    migration = AGENT_SKILLS_MIGRATIONS[agent_key]
+    console.print(f"\n[red]Error:[/red] {migration['error']}")
     console.print("Please use [cyan]--ai-skills[/cyan] when initializing to install templates as agent skills instead.")
-    console.print("[yellow]Usage:[/yellow] specify init <project> --ai agy --ai-skills")
+    console.print(f"[yellow]Usage:[/yellow] {migration['usage']}")
     raise typer.Exit(1)
 
 @app.command()
@@ -1467,7 +1492,7 @@ def init(
         specify init . --ai claude         # Initialize in current directory
         specify init .                     # Initialize in current directory (interactive AI selection)
         specify init --here --ai claude    # Alternative syntax for current directory
-        specify init --here --ai codex
+        specify init --here --ai codex --ai-skills
         specify init --here --ai codebuddy
         specify init --here --ai vibe      # Initialize with Mistral Vibe support
         specify init --here
@@ -1557,24 +1582,16 @@ def init(
             "copilot"
         )
 
-    # [DEPRECATION NOTICE: Antigravity (agy)]
-    # As of Antigravity v1.20.5, traditional CLI "command" support was fully removed
-    # in favor of "Agent Skills" (SKILL.md files under <agent_folder>/skills/<skill_name>/).
-    # Because 'specify_cli' historically populated .agent/commands/, we now must explicitly
-    # enforce the `--ai-skills` flag for `agy` to ensure valid template generation.
-    if selected_ai == "agy" and not ai_skills:
-        # If agy was selected interactively (no --ai provided), automatically enable
+    # Agents that have moved from explicit commands/prompts to agent skills.
+    if selected_ai in AGENT_SKILLS_MIGRATIONS and not ai_skills:
+        # If selected interactively (no --ai provided), automatically enable
         # ai_skills so the agent remains usable without requiring an extra flag.
-        # Preserve deprecation behavior only for explicit '--ai agy' without skills.
+        # Preserve fail-fast behavior only for explicit '--ai <agent>' without skills.
         if ai_assistant:
-            _handle_agy_deprecation(console)
+            _handle_agent_skills_migration(console, selected_ai)
         else:
             ai_skills = True
-            console.print(
-                "\n[yellow]Note:[/yellow] 'agy' was selected interactively; "
-                "enabling [cyan]--ai-skills[/cyan] automatically for compatibility "
-                "(explicit .agent/commands usage is deprecated)."
-            )
+            console.print(f"\n[yellow]Note:[/yellow] {AGENT_SKILLS_MIGRATIONS[selected_ai]['interactive_note']}")
 
     # Validate --ai-commands-dir usage
     if selected_ai == "generic":
@@ -1698,28 +1715,41 @@ def init(
             ensure_constitution_from_template(project_path, tracker=tracker)
 
             if ai_skills:
-                skills_ok = install_ai_skills(project_path, selected_ai, tracker=tracker)
+                if selected_ai in NATIVE_SKILLS_AGENTS:
+                    skills_dir = _get_skills_dir(project_path, selected_ai)
+                    if not _has_bundled_skills(project_path, selected_ai):
+                        raise RuntimeError(
+                            f"Expected bundled agent skills in {skills_dir.relative_to(project_path)}, "
+                            "but none were found. Re-run with an up-to-date template."
+                        )
+                    if tracker:
+                        tracker.start("ai-skills")
+                        tracker.complete("ai-skills", f"bundled skills → {skills_dir.relative_to(project_path)}")
+                    else:
+                        console.print(f"[green]✓[/green] Using bundled agent skills in {skills_dir.relative_to(project_path)}/")
+                else:
+                    skills_ok = install_ai_skills(project_path, selected_ai, tracker=tracker)
 
-                # When --ai-skills is used on a NEW project and skills were
-                # successfully installed, remove the command files that the
-                # template archive just created.  Skills replace commands, so
-                # keeping both would be confusing.  For --here on an existing
-                # repo we leave pre-existing commands untouched to avoid a
-                # breaking change.  We only delete AFTER skills succeed so the
-                # project always has at least one of {commands, skills}.
-                if skills_ok and not here:
-                    agent_cfg = AGENT_CONFIG.get(selected_ai, {})
-                    agent_folder = agent_cfg.get("folder", "")
-                    commands_subdir = agent_cfg.get("commands_subdir", "commands")
-                    if agent_folder:
-                        cmds_dir = project_path / agent_folder.rstrip("/") / commands_subdir
-                        if cmds_dir.exists():
-                            try:
-                                shutil.rmtree(cmds_dir)
-                            except OSError:
-                                # Best-effort cleanup: skills are already installed,
-                                # so leaving stale commands is non-fatal.
-                                console.print("[yellow]Warning: could not remove extracted commands directory[/yellow]")
+                    # When --ai-skills is used on a NEW project and skills were
+                    # successfully installed, remove the command files that the
+                    # template archive just created.  Skills replace commands, so
+                    # keeping both would be confusing.  For --here on an existing
+                    # repo we leave pre-existing commands untouched to avoid a
+                    # breaking change.  We only delete AFTER skills succeed so the
+                    # project always has at least one of {commands, skills}.
+                    if skills_ok and not here:
+                        agent_cfg = AGENT_CONFIG.get(selected_ai, {})
+                        agent_folder = agent_cfg.get("folder", "")
+                        commands_subdir = agent_cfg.get("commands_subdir", "commands")
+                        if agent_folder:
+                            cmds_dir = project_path / agent_folder.rstrip("/") / commands_subdir
+                            if cmds_dir.exists():
+                                try:
+                                    shutil.rmtree(cmds_dir)
+                                except OSError:
+                                    # Best-effort cleanup: skills are already installed,
+                                    # so leaving stale commands is non-fatal.
+                                    console.print("[yellow]Warning: could not remove extracted commands directory[/yellow]")
 
             if not no_git:
                 tracker.start("git")
@@ -1843,38 +1873,48 @@ def init(
         steps_lines.append("1. You're already in the project directory!")
         step_num = 2
 
-    # Add Codex-specific setup step if needed
-    if selected_ai == "codex":
-        codex_path = project_path / ".codex"
-        quoted_path = shlex.quote(str(codex_path))
-        if os.name == "nt":  # Windows
-            cmd = f"setx CODEX_HOME {quoted_path}"
-        else:  # Unix-like systems
-            cmd = f"export CODEX_HOME={quoted_path}"
-        
-        steps_lines.append(f"{step_num}. Set [cyan]CODEX_HOME[/cyan] environment variable before running Codex: [cyan]{cmd}[/cyan]")
+    if selected_ai == "codex" and ai_skills:
+        steps_lines.append(f"{step_num}. Start Codex in this project directory; spec-kit skills were installed to [cyan].agents/skills[/cyan]")
         step_num += 1
 
-    steps_lines.append(f"{step_num}. Start using slash commands with your AI agent:")
+    codex_skill_mode = selected_ai == "codex" and ai_skills
+    kimi_skill_mode = selected_ai == "kimi"
+    native_skill_mode = codex_skill_mode or kimi_skill_mode
+    usage_label = "skills" if native_skill_mode else "slash commands"
 
-    steps_lines.append("   2.1 [cyan]/speckit.constitution[/] - Establish project principles")
-    steps_lines.append("   2.2 [cyan]/speckit.specify[/] - Create baseline specification")
-    steps_lines.append("   2.3 [cyan]/speckit.plan[/] - Create implementation plan")
-    steps_lines.append("   2.4 [cyan]/speckit.tasks[/] - Generate actionable tasks")
-    steps_lines.append("   2.5 [cyan]/speckit.implement[/] - Execute implementation")
+    def _display_cmd(name: str) -> str:
+        if codex_skill_mode:
+            return f"$speckit-{name}"
+        if kimi_skill_mode:
+            return f"/skill:speckit.{name}"
+        return f"/speckit.{name}"
+
+    steps_lines.append(f"{step_num}. Start using {usage_label} with your AI agent:")
+
+    steps_lines.append(f"   {step_num}.1 [cyan]{_display_cmd('constitution')}[/] - Establish project principles")
+    steps_lines.append(f"   {step_num}.2 [cyan]{_display_cmd('specify')}[/] - Create baseline specification")
+    steps_lines.append(f"   {step_num}.3 [cyan]{_display_cmd('plan')}[/] - Create implementation plan")
+    steps_lines.append(f"   {step_num}.4 [cyan]{_display_cmd('tasks')}[/] - Generate actionable tasks")
+    steps_lines.append(f"   {step_num}.5 [cyan]{_display_cmd('implement')}[/] - Execute implementation")
 
     steps_panel = Panel("\n".join(steps_lines), title="Next Steps", border_style="cyan", padding=(1,2))
     console.print()
     console.print(steps_panel)
 
+    enhancement_intro = (
+        "Optional skills that you can use for your specs [bright_black](improve quality & confidence)[/bright_black]"
+        if native_skill_mode
+        else "Optional commands that you can use for your specs [bright_black](improve quality & confidence)[/bright_black]"
+    )
     enhancement_lines = [
-        "Optional commands that you can use for your specs [bright_black](improve quality & confidence)[/bright_black]",
+        enhancement_intro,
         "",
-        "○ [cyan]/speckit.clarify[/] [bright_black](optional)[/bright_black] - Ask structured questions to de-risk ambiguous areas before planning (run before [cyan]/speckit.plan[/] if used)",
-        "○ [cyan]/speckit.analyze[/] [bright_black](optional)[/bright_black] - Cross-artifact consistency & alignment report (after [cyan]/speckit.tasks[/], before [cyan]/speckit.implement[/])",
-        "○ [cyan]/speckit.checklist[/] [bright_black](optional)[/bright_black] - Generate quality checklists to validate requirements completeness, clarity, and consistency (after [cyan]/speckit.plan[/])"
+        f"○ [cyan]{_display_cmd('clarify')}[/] [bright_black](optional)[/bright_black] - Ask structured questions to de-risk ambiguous areas before planning (run before [cyan]{_display_cmd('plan')}[/] if used)",
+        f"○ [cyan]{_display_cmd('analyze')}[/] [bright_black](optional)[/bright_black] - Cross-artifact consistency & alignment report (after [cyan]{_display_cmd('tasks')}[/], before [cyan]{_display_cmd('implement')}[/])",
+        f"○ [cyan]{_display_cmd('checklist')}[/] [bright_black](optional)[/bright_black] - Generate quality checklists to validate requirements completeness, clarity, and consistency (after [cyan]{_display_cmd('plan')}[/])"
     ]
-    enhancements_panel = Panel("\n".join(enhancement_lines), title="Enhancement Commands", border_style="cyan", padding=(1,2))
+    enhancements_title = "Enhancement Skills" if native_skill_mode else "Enhancement Commands"
+    enhancements_panel = Panel("\n".join(enhancement_lines), title=enhancements_title, border_style="cyan", padding=(1,2))
     console.print()
     console.print(enhancements_panel)
 

src/specify_cli/agents.py

@@ -9,6 +9,7 @@ command files into agent-specific directories in the correct format.
 from pathlib import Path
 from typing import Dict, List, Any
 
+import platform
 import yaml
 
 
@@ -59,10 +60,10 @@ class CommandRegistrar:
             "extension": ".md"
         },
         "codex": {
-            "dir": ".codex/prompts",
+            "dir": ".agents/skills",
             "format": "markdown",
             "args": "$ARGUMENTS",
-            "extension": ".md"
+            "extension": "/SKILL.md",
         },
         "windsurf": {
             "dir": ".windsurf/workflows",
@@ -140,7 +141,7 @@ class CommandRegistrar:
             "dir": ".kimi/skills",
             "format": "markdown",
             "args": "$ARGUMENTS",
-            "extension": "/SKILL.md"
+            "extension": "/SKILL.md",
         },
         "trae": {
             "dir": ".trae/rules",
@@ -182,6 +183,9 @@ class CommandRegistrar:
         except yaml.YAMLError:
             frontmatter = {}
 
+        if not isinstance(frontmatter, dict):
+            frontmatter = {}
+
         return frontmatter, body
 
     @staticmethod
@@ -209,11 +213,14 @@ class CommandRegistrar:
         Returns:
             Modified frontmatter with adjusted paths
         """
-        if "scripts" in frontmatter:
-            for key in frontmatter["scripts"]:
-                script_path = frontmatter["scripts"][key]
-                if script_path.startswith("../../scripts/"):
-                    frontmatter["scripts"][key] = f".specify/scripts/{script_path[14:]}"
+        for script_key in ("scripts", "agent_scripts"):
+            scripts = frontmatter.get(script_key)
+            if not isinstance(scripts, dict):
+                continue
+
+            for key, script_path in scripts.items():
+                if isinstance(script_path, str) and script_path.startswith("../../scripts/"):
+                    scripts[key] = f".specify/scripts/{script_path[14:]}"
         return frontmatter
 
     def render_markdown_command(
@@ -270,6 +277,95 @@ class CommandRegistrar:
 
         return "\n".join(toml_lines)
 
+    def render_skill_command(
+        self,
+        agent_name: str,
+        skill_name: str,
+        frontmatter: dict,
+        body: str,
+        source_id: str,
+        source_file: str,
+        project_root: Path,
+    ) -> str:
+        """Render a command override as a SKILL.md file.
+
+        SKILL-target agents should receive the same skills-oriented
+        frontmatter shape used elsewhere in the project instead of the
+        original command frontmatter.
+        """
+        if not isinstance(frontmatter, dict):
+            frontmatter = {}
+
+        if agent_name == "codex":
+            body = self._resolve_codex_skill_placeholders(frontmatter, body, project_root)
+
+        description = frontmatter.get("description", f"Spec-kit workflow command: {skill_name}")
+        skill_frontmatter = {
+            "name": skill_name,
+            "description": description,
+            "compatibility": "Requires spec-kit project structure with .specify/ directory",
+            "metadata": {
+                "author": "github-spec-kit",
+                "source": f"{source_id}:{source_file}",
+            },
+        }
+        return self.render_frontmatter(skill_frontmatter) + "\n" + body
+
+    @staticmethod
+    def _resolve_codex_skill_placeholders(frontmatter: dict, body: str, project_root: Path) -> str:
+        """Resolve script placeholders for Codex skill overrides.
+
+        This intentionally scopes the fix to Codex, which is the newly
+        migrated runtime path in this PR. Existing Kimi behavior is left
+        unchanged for now.
+        """
+        try:
+            from . import load_init_options
+        except ImportError:
+            return body
+
+        if not isinstance(frontmatter, dict):
+            frontmatter = {}
+
+        scripts = frontmatter.get("scripts", {}) or {}
+        agent_scripts = frontmatter.get("agent_scripts", {}) or {}
+        if not isinstance(scripts, dict):
+            scripts = {}
+        if not isinstance(agent_scripts, dict):
+            agent_scripts = {}
+
+        script_variant = load_init_options(project_root).get("script")
+        if script_variant not in {"sh", "ps"}:
+            fallback_order = []
+            default_variant = "ps" if platform.system().lower().startswith("win") else "sh"
+            secondary_variant = "sh" if default_variant == "ps" else "ps"
+
+            if default_variant in scripts or default_variant in agent_scripts:
+                fallback_order.append(default_variant)
+            if secondary_variant in scripts or secondary_variant in agent_scripts:
+                fallback_order.append(secondary_variant)
+
+            for key in scripts:
+                if key not in fallback_order:
+                    fallback_order.append(key)
+            for key in agent_scripts:
+                if key not in fallback_order:
+                    fallback_order.append(key)
+
+            script_variant = fallback_order[0] if fallback_order else None
+
+        script_command = scripts.get(script_variant) if script_variant else None
+        if script_command:
+            script_command = script_command.replace("{ARGS}", "$ARGUMENTS")
+            body = body.replace("{SCRIPT}", script_command)
+
+        agent_script_command = agent_scripts.get(script_variant) if script_variant else None
+        if agent_script_command:
+            agent_script_command = agent_script_command.replace("{ARGS}", "$ARGUMENTS")
+            body = body.replace("{AGENT_SCRIPT}", agent_script_command)
+
+        return body.replace("{ARGS}", "$ARGUMENTS").replace("__AGENT__", "codex")
+
     def _convert_argument_placeholder(self, content: str, from_placeholder: str, to_placeholder: str) -> str:
         """Convert argument placeholder format.
 
@@ -283,6 +379,18 @@ class CommandRegistrar:
         """
         return content.replace(from_placeholder, to_placeholder)
 
+    @staticmethod
+    def _compute_output_name(agent_name: str, cmd_name: str, agent_config: Dict[str, Any]) -> str:
+        """Compute the on-disk command or skill name for an agent."""
+        if agent_config["extension"] != "/SKILL.md":
+            return cmd_name
+
+        short_name = cmd_name
+        if short_name.startswith("speckit."):
+            short_name = short_name[len("speckit."):]
+
+        return f"speckit.{short_name}" if agent_name == "kimi" else f"speckit-{short_name}"
+
     def register_commands(
         self,
         agent_name: str,
@@ -334,14 +442,20 @@ class CommandRegistrar:
                 body, "$ARGUMENTS", agent_config["args"]
             )
 
-            if agent_config["format"] == "markdown":
+            output_name = self._compute_output_name(agent_name, cmd_name, agent_config)
+
+            if agent_config["extension"] == "/SKILL.md":
+                output = self.render_skill_command(
+                    agent_name, output_name, frontmatter, body, source_id, cmd_file, project_root
+                )
+            elif agent_config["format"] == "markdown":
                 output = self.render_markdown_command(frontmatter, body, source_id, context_note)
             elif agent_config["format"] == "toml":
                 output = self.render_toml_command(frontmatter, body, source_id)
             else:
                 raise ValueError(f"Unsupported format: {agent_config['format']}")
 
-            dest_file = commands_dir / f"{cmd_name}{agent_config['extension']}"
+            dest_file = commands_dir / f"{output_name}{agent_config['extension']}"
             dest_file.parent.mkdir(parents=True, exist_ok=True)
             dest_file.write_text(output, encoding="utf-8")
 
@@ -351,9 +465,15 @@ class CommandRegistrar:
             registered.append(cmd_name)
 
             for alias in cmd_info.get("aliases", []):
-                alias_file = commands_dir / f"{alias}{agent_config['extension']}"
+                alias_output_name = self._compute_output_name(agent_name, alias, agent_config)
+                alias_output = output
+                if agent_config["extension"] == "/SKILL.md":
+                    alias_output = self.render_skill_command(
+                        agent_name, alias_output_name, frontmatter, body, source_id, cmd_file, project_root
+                    )
+                alias_file = commands_dir / f"{alias_output_name}{agent_config['extension']}"
                 alias_file.parent.mkdir(parents=True, exist_ok=True)
-                alias_file.write_text(output, encoding="utf-8")
+                alias_file.write_text(alias_output, encoding="utf-8")
                 if agent_name == "copilot":
                     self.write_copilot_prompt(project_root, alias)
                 registered.append(alias)
@@ -396,7 +516,7 @@ class CommandRegistrar:
         results = {}
 
         for agent_name, agent_config in self.AGENT_CONFIGS.items():
-            agent_dir = project_root / agent_config["dir"].split("/")[0]
+            agent_dir = project_root / agent_config["dir"]
 
             if agent_dir.exists():
                 try:
@@ -430,7 +550,8 @@ class CommandRegistrar:
             commands_dir = project_root / agent_config["dir"]
 
             for cmd_name in cmd_names:
-                cmd_file = commands_dir / f"{cmd_name}{agent_config['extension']}"
+                output_name = self._compute_output_name(agent_name, cmd_name, agent_config)
+                cmd_file = commands_dir / f"{output_name}{agent_config['extension']}"
                 if cmd_file.exists():
                     cmd_file.unlink()
 

src/specify_cli/presets.py

@@ -646,8 +646,6 @@ class PresetManager:
             short_name = cmd_name
             if short_name.startswith("speckit."):
                 short_name = short_name[len("speckit."):]
-            # Kimi CLI discovers skills by directory name and invokes them as
-            # /skill:<name> — use dot separator to match packaging convention.
             if selected_ai == "kimi":
                 skill_name = f"speckit.{short_name}"
             else:

tests/test_agent_config_consistency.py

@@ -29,11 +29,17 @@ class TestAgentConfigConsistency:
         assert "q" not in cfg
 
     def test_extension_registrar_includes_codex(self):
-        """Extension command registrar should include codex targeting .codex/prompts."""
+        """Extension command registrar should include codex targeting .agents/skills."""
         cfg = CommandRegistrar.AGENT_CONFIGS
 
         assert "codex" in cfg
-        assert cfg["codex"]["dir"] == ".codex/prompts"
+        assert cfg["codex"]["dir"] == ".agents/skills"
+        assert cfg["codex"]["extension"] == "/SKILL.md"
+
+    def test_runtime_codex_uses_native_skills(self):
+        """Codex runtime config should point at .agents/skills."""
+        assert AGENT_CONFIG["codex"]["folder"] == ".agents/"
+        assert AGENT_CONFIG["codex"]["commands_subdir"] == "skills"
 
     def test_release_agent_lists_include_kiro_cli_and_exclude_q(self):
         """Bash and PowerShell release scripts should agree on agent key set for Kiro."""
@@ -71,6 +77,16 @@ class TestAgentConfigConsistency:
         assert re.search(r"shai\)\s*\n.*?\.shai/commands", sh_text, re.S) is not None
         assert re.search(r"agy\)\s*\n.*?\.agent/commands", sh_text, re.S) is not None
 
+    def test_release_scripts_generate_codex_skills(self):
+        """Release scripts should generate Codex skills in .agents/skills."""
+        sh_text = (REPO_ROOT / ".github" / "workflows" / "scripts" / "create-release-packages.sh").read_text(encoding="utf-8")
+        ps_text = (REPO_ROOT / ".github" / "workflows" / "scripts" / "create-release-packages.ps1").read_text(encoding="utf-8")
+
+        assert ".agents/skills" in sh_text
+        assert ".agents/skills" in ps_text
+        assert re.search(r"codex\)\s*\n.*?create_skills.*?\.agents/skills.*?\"-\"", sh_text, re.S) is not None
+        assert re.search(r"'codex'\s*\{.*?\.agents/skills.*?New-Skills.*?-Separator '-'", ps_text, re.S) is not None
+
     def test_init_ai_help_includes_roo_and_kiro_alias(self):
         """CLI help text for --ai should stay in sync with agent config and alias guidance."""
         assert "roo" in AI_ASSISTANT_HELP

tests/test_ai_skills.py

@@ -471,8 +471,7 @@ class TestInstallAiSkills:
         skills_dir = _get_skills_dir(proj, agent_key)
         assert skills_dir.exists()
         skill_dirs = [d.name for d in skills_dir.iterdir() if d.is_dir()]
-        # Kimi uses dot-separator (speckit.specify) to match /skill:speckit.* invocation;
-        # all other agents use hyphen-separator (speckit-specify).
+        # Kimi uses dotted skill names; other agents use hyphen-separated names.
         expected_skill_name = "speckit.specify" if agent_key == "kimi" else "speckit-specify"
         assert expected_skill_name in skill_dirs
         assert (skills_dir / expected_skill_name / "SKILL.md").exists()
@@ -694,6 +693,82 @@ class TestNewProjectCommandSkip:
         prompts_dir = target / ".kiro" / "prompts"
         assert not prompts_dir.exists()
 
+    def test_codex_native_skills_preserved_without_conversion(self, tmp_path):
+        """Codex should keep bundled .agents/skills and skip install_ai_skills conversion."""
+        from typer.testing import CliRunner
+
+        runner = CliRunner()
+        target = tmp_path / "new-codex-proj"
+
+        def fake_download(project_path, *args, **kwargs):
+            skill_dir = project_path / ".agents" / "skills" / "speckit-specify"
+            skill_dir.mkdir(parents=True, exist_ok=True)
+            (skill_dir / "SKILL.md").write_text("---\ndescription: Test skill\n---\n\nBody.\n")
+
+        with patch("specify_cli.download_and_extract_template", side_effect=fake_download), \
+             patch("specify_cli.ensure_executable_scripts"), \
+             patch("specify_cli.ensure_constitution_from_template"), \
+             patch("specify_cli.install_ai_skills") as mock_skills, \
+             patch("specify_cli.is_git_repo", return_value=False), \
+             patch("specify_cli.shutil.which", return_value="/usr/bin/codex"):
+            result = runner.invoke(
+                app,
+                ["init", str(target), "--ai", "codex", "--ai-skills", "--script", "sh", "--no-git"],
+            )
+
+        assert result.exit_code == 0
+        mock_skills.assert_not_called()
+        assert (target / ".agents" / "skills" / "speckit-specify" / "SKILL.md").exists()
+
+    def test_codex_native_skills_missing_fails_clearly(self, tmp_path):
+        """Codex native skills init should fail if bundled skills are missing."""
+        from typer.testing import CliRunner
+
+        runner = CliRunner()
+        target = tmp_path / "missing-codex-skills"
+
+        with patch("specify_cli.download_and_extract_template", lambda *args, **kwargs: None), \
+             patch("specify_cli.ensure_executable_scripts"), \
+             patch("specify_cli.ensure_constitution_from_template"), \
+             patch("specify_cli.install_ai_skills") as mock_skills, \
+             patch("specify_cli.is_git_repo", return_value=False), \
+             patch("specify_cli.shutil.which", return_value="/usr/bin/codex"):
+            result = runner.invoke(
+                app,
+                ["init", str(target), "--ai", "codex", "--ai-skills", "--script", "sh", "--no-git"],
+            )
+
+        assert result.exit_code == 1
+        mock_skills.assert_not_called()
+        assert "Expected bundled agent skills" in result.output
+
+    def test_codex_native_skills_ignores_non_speckit_skill_dirs(self, tmp_path):
+        """Non-spec-kit SKILL.md files should not satisfy Codex bundled-skills validation."""
+        from typer.testing import CliRunner
+
+        runner = CliRunner()
+        target = tmp_path / "foreign-codex-skills"
+
+        def fake_download(project_path, *args, **kwargs):
+            skill_dir = project_path / ".agents" / "skills" / "other-tool"
+            skill_dir.mkdir(parents=True, exist_ok=True)
+            (skill_dir / "SKILL.md").write_text("---\ndescription: Foreign skill\n---\n\nBody.\n")
+
+        with patch("specify_cli.download_and_extract_template", side_effect=fake_download), \
+             patch("specify_cli.ensure_executable_scripts"), \
+             patch("specify_cli.ensure_constitution_from_template"), \
+             patch("specify_cli.install_ai_skills") as mock_skills, \
+             patch("specify_cli.is_git_repo", return_value=False), \
+             patch("specify_cli.shutil.which", return_value="/usr/bin/codex"):
+            result = runner.invoke(
+                app,
+                ["init", str(target), "--ai", "codex", "--ai-skills", "--script", "sh", "--no-git"],
+            )
+
+        assert result.exit_code == 1
+        mock_skills.assert_not_called()
+        assert "Expected bundled agent skills" in result.output
+
     def test_commands_preserved_when_skills_fail(self, tmp_path):
         """If skills fail, commands should NOT be removed (safety net)."""
         from typer.testing import CliRunner
@@ -837,6 +912,17 @@ class TestCliValidation:
         assert "Explicit command support was deprecated in Antigravity version 1.20.5." in result.output
         assert "--ai-skills" in result.output
 
+    def test_codex_without_ai_skills_fails(self):
+        """--ai codex without --ai-skills should fail with exit code 1."""
+        from typer.testing import CliRunner
+
+        runner = CliRunner()
+        result = runner.invoke(app, ["init", "test-proj", "--ai", "codex"])
+
+        assert result.exit_code == 1
+        assert "Custom prompt-based spec-kit initialization is deprecated for Codex CLI" in result.output
+        assert "--ai-skills" in result.output
+
     def test_interactive_agy_without_ai_skills_prompts_skills(self, monkeypatch):
         """Interactive selector returning agy without --ai-skills should automatically enable --ai-skills."""
         from typer.testing import CliRunner
@@ -879,6 +965,72 @@ class TestCliValidation:
             assert result.exit_code == 0
             assert "Explicit command support was deprecated" not in result.output
 
+    def test_interactive_codex_without_ai_skills_enables_skills(self, monkeypatch):
+        """Interactive selector returning codex without --ai-skills should automatically enable --ai-skills."""
+        from typer.testing import CliRunner
+
+        def _fake_select_with_arrows(*args, **kwargs):
+            options = kwargs.get("options")
+            if options is None and len(args) >= 1:
+                options = args[0]
+
+            if isinstance(options, dict) and "codex" in options:
+                return "codex"
+            if isinstance(options, (list, tuple)) and "codex" in options:
+                return "codex"
+
+            if isinstance(options, dict) and options:
+                return next(iter(options.keys()))
+            if isinstance(options, (list, tuple)) and options:
+                return options[0]
+
+            return None
+
+        monkeypatch.setattr("specify_cli.select_with_arrows", _fake_select_with_arrows)
+
+        def _fake_download(*args, **kwargs):
+            project_path = Path(args[0])
+            skill_dir = project_path / ".agents" / "skills" / "speckit-specify"
+            skill_dir.mkdir(parents=True, exist_ok=True)
+            (skill_dir / "SKILL.md").write_text("---\ndescription: Test skill\n---\n\nBody.\n")
+
+        monkeypatch.setattr("specify_cli.download_and_extract_template", _fake_download)
+
+        runner = CliRunner()
+        with runner.isolated_filesystem():
+            result = runner.invoke(app, ["init", "test-proj", "--no-git", "--ignore-agent-tools"])
+
+            assert result.exit_code == 0
+            assert "Custom prompt-based spec-kit initialization is deprecated for Codex CLI" not in result.output
+            assert ".agents/skills" in result.output
+            assert "$speckit-constitution" in result.output
+            assert "/speckit.constitution" not in result.output
+            assert "Optional skills that you can use for your specs" in result.output
+
+    def test_kimi_next_steps_show_skill_invocation(self, monkeypatch):
+        """Kimi next-steps guidance should display /skill:speckit.* usage."""
+        from typer.testing import CliRunner
+
+        def _fake_download(*args, **kwargs):
+            project_path = Path(args[0])
+            skill_dir = project_path / ".kimi" / "skills" / "speckit.specify"
+            skill_dir.mkdir(parents=True, exist_ok=True)
+            (skill_dir / "SKILL.md").write_text("---\ndescription: Test skill\n---\n\nBody.\n")
+
+        monkeypatch.setattr("specify_cli.download_and_extract_template", _fake_download)
+
+        runner = CliRunner()
+        with runner.isolated_filesystem():
+            result = runner.invoke(
+                app,
+                ["init", "test-proj", "--ai", "kimi", "--no-git", "--ignore-agent-tools"],
+            )
+
+            assert result.exit_code == 0
+            assert "/skill:speckit.constitution" in result.output
+            assert "/speckit.constitution" not in result.output
+            assert "Optional skills that you can use for your specs" in result.output
+
     def test_ai_skills_flag_appears_in_help(self):
         """--ai-skills should appear in init --help output."""
         from typer.testing import CliRunner

tests/test_extensions.py

@@ -665,9 +665,10 @@ class TestCommandRegistrar:
         assert "q" not in CommandRegistrar.AGENT_CONFIGS
 
     def test_codex_agent_config_present(self):
-        """Codex should be mapped to .codex/prompts."""
+        """Codex should be mapped to .agents/skills."""
         assert "codex" in CommandRegistrar.AGENT_CONFIGS
-        assert CommandRegistrar.AGENT_CONFIGS["codex"]["dir"] == ".codex/prompts"
+        assert CommandRegistrar.AGENT_CONFIGS["codex"]["dir"] == ".agents/skills"
+        assert CommandRegistrar.AGENT_CONFIGS["codex"]["extension"] == "/SKILL.md"
 
     def test_pi_agent_config_present(self):
         """Pi should be mapped to .pi/prompts."""
@@ -717,6 +718,21 @@ $ARGUMENTS
         assert frontmatter == {}
         assert body == content
 
+    def test_parse_frontmatter_non_mapping_returns_empty_dict(self):
+        """Non-mapping YAML frontmatter should not crash downstream renderers."""
+        content = """---
+- item1
+- item2
+---
+
+# Command body
+"""
+        registrar = CommandRegistrar()
+        frontmatter, body = registrar.parse_frontmatter(content)
+
+        assert frontmatter == {}
+        assert "Command body" in body
+
     def test_render_frontmatter(self):
         """Test rendering frontmatter to YAML."""
         frontmatter = {
@@ -808,6 +824,299 @@ $ARGUMENTS
         assert (claude_dir / "speckit.alias.cmd.md").exists()
         assert (claude_dir / "speckit.shortcut.md").exists()
 
+    def test_unregister_commands_for_codex_skills_uses_mapped_names(self, project_dir):
+        """Codex skill cleanup should use the same mapped names as registration."""
+        skills_dir = project_dir / ".agents" / "skills"
+        (skills_dir / "speckit-specify").mkdir(parents=True)
+        (skills_dir / "speckit-specify" / "SKILL.md").write_text("body")
+        (skills_dir / "speckit-shortcut").mkdir(parents=True)
+        (skills_dir / "speckit-shortcut" / "SKILL.md").write_text("body")
+
+        registrar = CommandRegistrar()
+        registrar.unregister_commands(
+            {"codex": ["speckit.specify", "speckit.shortcut"]},
+            project_dir,
+        )
+
+        assert not (skills_dir / "speckit-specify" / "SKILL.md").exists()
+        assert not (skills_dir / "speckit-shortcut" / "SKILL.md").exists()
+
+    def test_register_commands_for_all_agents_distinguishes_codex_from_amp(self, extension_dir, project_dir):
+        """A Codex project under .agents/skills should not implicitly activate Amp."""
+        skills_dir = project_dir / ".agents" / "skills"
+        skills_dir.mkdir(parents=True)
+
+        manifest = ExtensionManifest(extension_dir / "extension.yml")
+        registrar = CommandRegistrar()
+        registered = registrar.register_commands_for_all_agents(manifest, extension_dir, project_dir)
+
+        assert "codex" in registered
+        assert "amp" not in registered
+        assert not (project_dir / ".agents" / "commands").exists()
+
+    def test_codex_skill_registration_writes_skill_frontmatter(self, extension_dir, project_dir):
+        """Codex SKILL.md output should use skills-oriented frontmatter."""
+        skills_dir = project_dir / ".agents" / "skills"
+        skills_dir.mkdir(parents=True)
+
+        manifest = ExtensionManifest(extension_dir / "extension.yml")
+        registrar = CommandRegistrar()
+        registrar.register_commands_for_agent("codex", manifest, extension_dir, project_dir)
+
+        skill_file = skills_dir / "speckit-test.hello" / "SKILL.md"
+        assert skill_file.exists()
+
+        content = skill_file.read_text()
+        assert "name: speckit-test.hello" in content
+        assert "description: Test hello command" in content
+        assert "compatibility:" in content
+        assert "metadata:" in content
+        assert "source: test-ext:commands/hello.md" in content
+        assert "<!-- Extension:" not in content
+
+    def test_codex_skill_registration_resolves_script_placeholders(self, project_dir, temp_dir):
+        """Codex SKILL.md overrides should resolve script placeholders."""
+        import yaml
+
+        ext_dir = temp_dir / "ext-scripted"
+        ext_dir.mkdir()
+        (ext_dir / "commands").mkdir()
+
+        manifest_data = {
+            "schema_version": "1.0",
+            "extension": {
+                "id": "ext-scripted",
+                "name": "Scripted Extension",
+                "version": "1.0.0",
+                "description": "Test",
+            },
+            "requires": {"speckit_version": ">=0.1.0"},
+            "provides": {
+                "commands": [
+                    {
+                        "name": "speckit.test.plan",
+                        "file": "commands/plan.md",
+                        "description": "Scripted command",
+                    }
+                ]
+            },
+        }
+        with open(ext_dir / "extension.yml", "w") as f:
+            yaml.dump(manifest_data, f)
+
+        (ext_dir / "commands" / "plan.md").write_text(
+            """---
+description: "Scripted command"
+scripts:
+  sh: ../../scripts/bash/setup-plan.sh --json "{ARGS}"
+  ps: ../../scripts/powershell/setup-plan.ps1 -Json
+agent_scripts:
+  sh: ../../scripts/bash/update-agent-context.sh __AGENT__
+  ps: ../../scripts/powershell/update-agent-context.ps1 -AgentType __AGENT__
+---
+
+Run {SCRIPT}
+Then {AGENT_SCRIPT}
+Agent __AGENT__
+"""
+        )
+
+        init_options = project_dir / ".specify" / "init-options.json"
+        init_options.parent.mkdir(parents=True, exist_ok=True)
+        init_options.write_text('{"ai":"codex","ai_skills":true,"script":"sh"}')
+
+        skills_dir = project_dir / ".agents" / "skills"
+        skills_dir.mkdir(parents=True)
+
+        manifest = ExtensionManifest(ext_dir / "extension.yml")
+        registrar = CommandRegistrar()
+        registrar.register_commands_for_agent("codex", manifest, ext_dir, project_dir)
+
+        skill_file = skills_dir / "speckit-test.plan" / "SKILL.md"
+        assert skill_file.exists()
+
+        content = skill_file.read_text()
+        assert "{SCRIPT}" not in content
+        assert "{AGENT_SCRIPT}" not in content
+        assert "__AGENT__" not in content
+        assert "{ARGS}" not in content
+        assert '.specify/scripts/bash/setup-plan.sh --json "$ARGUMENTS"' in content
+        assert ".specify/scripts/bash/update-agent-context.sh codex" in content
+
+    def test_codex_skill_alias_frontmatter_matches_alias_name(self, project_dir, temp_dir):
+        """Codex alias skills should render their own matching `name:` frontmatter."""
+        import yaml
+
+        ext_dir = temp_dir / "ext-alias-skill"
+        ext_dir.mkdir()
+        (ext_dir / "commands").mkdir()
+
+        manifest_data = {
+            "schema_version": "1.0",
+            "extension": {
+                "id": "ext-alias-skill",
+                "name": "Alias Skill Extension",
+                "version": "1.0.0",
+                "description": "Test",
+            },
+            "requires": {"speckit_version": ">=0.1.0"},
+            "provides": {
+                "commands": [
+                    {
+                        "name": "speckit.alias.cmd",
+                        "file": "commands/cmd.md",
+                        "aliases": ["speckit.shortcut"],
+                    }
+                ]
+            },
+        }
+        with open(ext_dir / "extension.yml", "w") as f:
+            yaml.dump(manifest_data, f)
+
+        (ext_dir / "commands" / "cmd.md").write_text("---\ndescription: Alias skill\n---\n\nBody\n")
+
+        skills_dir = project_dir / ".agents" / "skills"
+        skills_dir.mkdir(parents=True)
+
+        manifest = ExtensionManifest(ext_dir / "extension.yml")
+        registrar = CommandRegistrar()
+        registrar.register_commands_for_agent("codex", manifest, ext_dir, project_dir)
+
+        primary = skills_dir / "speckit-alias.cmd" / "SKILL.md"
+        alias = skills_dir / "speckit-shortcut" / "SKILL.md"
+
+        assert primary.exists()
+        assert alias.exists()
+        assert "name: speckit-alias.cmd" in primary.read_text()
+        assert "name: speckit-shortcut" in alias.read_text()
+
+    def test_codex_skill_registration_uses_fallback_script_variant_without_init_options(
+        self, project_dir, temp_dir
+    ):
+        """Codex placeholder substitution should still work without init-options.json."""
+        import yaml
+
+        ext_dir = temp_dir / "ext-script-fallback"
+        ext_dir.mkdir()
+        (ext_dir / "commands").mkdir()
+
+        manifest_data = {
+            "schema_version": "1.0",
+            "extension": {
+                "id": "ext-script-fallback",
+                "name": "Script fallback",
+                "version": "1.0.0",
+                "description": "Test",
+            },
+            "requires": {"speckit_version": ">=0.1.0"},
+            "provides": {
+                "commands": [
+                    {
+                        "name": "speckit.fallback.plan",
+                        "file": "commands/plan.md",
+                    }
+                ]
+            },
+        }
+        with open(ext_dir / "extension.yml", "w") as f:
+            yaml.dump(manifest_data, f)
+
+        (ext_dir / "commands" / "plan.md").write_text(
+            """---
+description: "Fallback scripted command"
+scripts:
+  sh: ../../scripts/bash/setup-plan.sh --json "{ARGS}"
+  ps: ../../scripts/powershell/setup-plan.ps1 -Json
+agent_scripts:
+  sh: ../../scripts/bash/update-agent-context.sh __AGENT__
+---
+
+Run {SCRIPT}
+Then {AGENT_SCRIPT}
+"""
+        )
+
+        # Intentionally do NOT create .specify/init-options.json
+        skills_dir = project_dir / ".agents" / "skills"
+        skills_dir.mkdir(parents=True)
+
+        manifest = ExtensionManifest(ext_dir / "extension.yml")
+        registrar = CommandRegistrar()
+        registrar.register_commands_for_agent("codex", manifest, ext_dir, project_dir)
+
+        skill_file = skills_dir / "speckit-fallback.plan" / "SKILL.md"
+        assert skill_file.exists()
+
+        content = skill_file.read_text()
+        assert "{SCRIPT}" not in content
+        assert "{AGENT_SCRIPT}" not in content
+        assert '.specify/scripts/bash/setup-plan.sh --json "$ARGUMENTS"' in content
+        assert ".specify/scripts/bash/update-agent-context.sh codex" in content
+
+    def test_codex_skill_registration_fallback_prefers_powershell_on_windows(
+        self, project_dir, temp_dir, monkeypatch
+    ):
+        """Without init metadata, Windows fallback should prefer ps scripts over sh."""
+        import yaml
+
+        monkeypatch.setattr("specify_cli.agents.platform.system", lambda: "Windows")
+
+        ext_dir = temp_dir / "ext-script-windows-fallback"
+        ext_dir.mkdir()
+        (ext_dir / "commands").mkdir()
+
+        manifest_data = {
+            "schema_version": "1.0",
+            "extension": {
+                "id": "ext-script-windows-fallback",
+                "name": "Script fallback windows",
+                "version": "1.0.0",
+                "description": "Test",
+            },
+            "requires": {"speckit_version": ">=0.1.0"},
+            "provides": {
+                "commands": [
+                    {
+                        "name": "speckit.windows.plan",
+                        "file": "commands/plan.md",
+                    }
+                ]
+            },
+        }
+        with open(ext_dir / "extension.yml", "w") as f:
+            yaml.dump(manifest_data, f)
+
+        (ext_dir / "commands" / "plan.md").write_text(
+            """---
+description: "Windows fallback scripted command"
+scripts:
+  sh: ../../scripts/bash/setup-plan.sh --json "{ARGS}"
+  ps: ../../scripts/powershell/setup-plan.ps1 -Json
+agent_scripts:
+  sh: ../../scripts/bash/update-agent-context.sh __AGENT__
+  ps: ../../scripts/powershell/update-agent-context.ps1 -AgentType __AGENT__
+---
+
+Run {SCRIPT}
+Then {AGENT_SCRIPT}
+"""
+        )
+
+        skills_dir = project_dir / ".agents" / "skills"
+        skills_dir.mkdir(parents=True)
+
+        manifest = ExtensionManifest(ext_dir / "extension.yml")
+        registrar = CommandRegistrar()
+        registrar.register_commands_for_agent("codex", manifest, ext_dir, project_dir)
+
+        skill_file = skills_dir / "speckit-windows.plan" / "SKILL.md"
+        assert skill_file.exists()
+
+        content = skill_file.read_text()
+        assert ".specify/scripts/powershell/setup-plan.ps1 -Json" in content
+        assert ".specify/scripts/powershell/update-agent-context.ps1 -AgentType codex" in content
+        assert ".specify/scripts/bash/setup-plan.sh" not in content
+
     def test_register_commands_for_copilot(self, extension_dir, project_dir):
         """Test registering commands for Copilot agent with .agent.md extension."""
         # Create .github/agents directory (Copilot project)