fix(codex): inject dot-to-hyphen hook command note in Codex skills (#2503)

* fix(codex): inject dot-to-hyphen hook command note in Codex skills

Hook commands in `.specify/extensions.yml` use dotted ids like
`speckit.git.commit`, but Codex skills are named with hyphens
(`speckit-git-commit`). The Claude integration handles this via an
explicit instruction injected into each generated SKILL.md by
`ClaudeIntegration.post_process_skill_content`, but the Codex
integration had no such override, so Codex would emit
`/speckit.git.commit` (which does not resolve) instead of
`/speckit-git-commit`.

This adds the same `_inject_hook_command_note` helper and a
`post_process_skill_content` override to `CodexIntegration`, plus a
small `setup()` override that applies the post-process to each
generated SKILL.md (mirroring the pattern in `ClaudeIntegration`).

Also widens the existing
`test_non_claude_post_process_is_identity` test to use `agy`
(another `SkillsIntegration` with no override), since asserting
identity behavior on Codex would now incorrectly fail.

Tests:
- New `TestCodexHookCommandNote` class mirrors
  `TestClaudeHookCommandNote`: setup-level injection, no-op when
  no hook block is present, idempotency, and indentation
  preservation.
- `pytest tests/` → 2866 passed, 34 skipped.

Signed-off-by: Chao Zhang <1175468+picklebento@users.noreply.github.com>

* fix(codex): handle empty eol when instruction is final line without newline

The hook-note injection regex allowed end-of-string matches via ``$``,
which left the captured ``eol`` empty. When the matched indent was also
empty, the substitution concatenated the note onto the same line as the
instruction. Default ``eol`` to ``\n`` when the capture is empty.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

---------

Signed-off-by: Chao Zhang <1175468+picklebento@users.noreply.github.com>
Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>

tests/integrations/test_integration_claude.py

@@ -487,13 +487,15 @@ class TestClaudeDisableModelInvocation:
         assert "disable-model-invocation" not in fm
         assert "user-invocable" not in fm
 
-    def test_non_claude_post_process_is_identity(self, tmp_path):
-        """Non-Claude integrations should not modify skill content."""
-        codex = get_integration("codex")
-        if codex is None:
-            return  # codex not registered in this build
+    def test_skills_default_post_process_is_identity(self, tmp_path):
+        """SkillsIntegration agents without an override leave content unchanged."""
+        # ``agy`` is a plain SkillsIntegration with no post-process override,
+        # so it stands in for the base-class default behavior.
+        agy = get_integration("agy")
+        if agy is None:
+            return  # agy not registered in this build
         content = "---\nname: test\n---\nBody"
-        assert codex.post_process_skill_content(content) == content
+        assert agy.post_process_skill_content(content) == content
 
 
 class TestClaudeHookCommandNote:

tests/integrations/test_integration_codex.py

@@ -1,5 +1,8 @@
 """Tests for CodexIntegration."""
 
+from specify_cli.integrations import get_integration
+from specify_cli.integrations.manifest import IntegrationManifest
+
 from .test_integration_base_skills import SkillsIntegrationTests
 
 
@@ -25,3 +28,89 @@ class TestCodexAutoPromote:
 
         assert result.exit_code == 0, f"init --ai codex failed: {result.output}"
         assert (target / ".agents" / "skills" / "speckit-plan" / "SKILL.md").exists()
+
+
+class TestCodexHookCommandNote:
+    """Verify dot-to-hyphen normalization note is injected in hook sections.
+
+    Hook commands in ``extensions.yml`` use dotted ids like
+    ``speckit.git.commit`` but Codex skills are named with hyphens
+    (``speckit-git-commit``). Without this note, Codex emits
+    ``/speckit.git.commit``, which does not resolve.
+    """
+
+    def test_hook_note_injected_in_skills_with_hooks(self, tmp_path):
+        """Skills that have hook sections should get the normalization note."""
+        i = get_integration("codex")
+        m = IntegrationManifest("codex", tmp_path)
+        i.setup(tmp_path, m, script_type="sh")
+        specify_skill = tmp_path / ".agents/skills/speckit-specify/SKILL.md"
+        assert specify_skill.exists()
+        content = specify_skill.read_text(encoding="utf-8")
+        assert "replace dots" in content, (
+            "speckit-specify should have dot-to-hyphen hook note"
+        )
+
+    def test_hook_note_not_in_skills_without_hooks(self):
+        """Skills without hook sections should not get the note."""
+        from specify_cli.integrations.codex import CodexIntegration
+
+        content = "---\nname: test\ndescription: test\n---\n\nNo hooks here.\n"
+        result = CodexIntegration._inject_hook_command_note(content)
+        assert "replace dots" not in result
+
+    def test_hook_note_idempotent(self):
+        """Injecting the note twice should not duplicate it."""
+        from specify_cli.integrations.codex import CodexIntegration
+
+        content = (
+            "---\nname: test\n---\n\n"
+            "- For each executable hook, output the following based on its flag:\n"
+        )
+        once = CodexIntegration._inject_hook_command_note(content)
+        twice = CodexIntegration._inject_hook_command_note(once)
+        assert once == twice, "Hook note injection should be idempotent"
+
+    def test_hook_note_preserves_indentation(self):
+        """The injected note should match the indentation of the target line."""
+        from specify_cli.integrations.codex import CodexIntegration
+
+        content = (
+            "---\nname: test\n---\n\n"
+            "   - For each executable hook, output the following\n"
+        )
+        result = CodexIntegration._inject_hook_command_note(content)
+        lines = result.splitlines()
+        note_line = [l for l in lines if "replace dots" in l][0]
+        assert note_line.startswith("   "), "Note should preserve indentation"
+
+    def test_hook_note_when_instruction_is_final_line_without_newline(self):
+        """Note must not collapse onto the instruction line when the file
+        ends without a trailing newline and the preceding line is not blank.
+        """
+        from specify_cli.integrations.codex import CodexIntegration
+
+        # No blank line before the instruction and no trailing newline:
+        # this is the case where the captured ``eol`` is empty and the
+        # captured indent is also empty, so a missing line separator would
+        # cause the note and instruction to collapse onto one line.
+        content = (
+            "---\nname: test\n---\n"
+            "Body line\n"
+            "- For each executable hook, output the following"
+        )
+        result = CodexIntegration._inject_hook_command_note(content)
+        lines = result.splitlines()
+        note_line_idx = next(
+            i for i, l in enumerate(lines) if "replace dots" in l
+        )
+        instruction_line_idx = next(
+            i for i, l in enumerate(lines)
+            if l.lstrip().startswith("- For each executable hook")
+        )
+        assert note_line_idx < instruction_line_idx, (
+            "Note must appear before the instruction"
+        )
+        assert "For each executable hook" not in lines[note_line_idx], (
+            "Note and instruction must not be on the same line"
+        )