fix(cli): honor editor_files opt-outs during init and update

packages/cli/src/repowise/cli/editor_integrations/codex.py

@@ -37,15 +37,16 @@ def write_project_files(
         setup_override = options.integration_overrides.get(self.integration_id)
         agents_override = options.project_file_overrides.get(self.project_file_id)
         agents_override_present = self.project_file_id in options.project_file_overrides
+        agents_disabled = self.project_file_id in options.disabled_project_files
         # Codex is opt-in, and stays that way. It is the one integration that
         # already got this right — nothing is written unless --codex or the
         # checklist asked for it — which is why #1499 names the other two.
         if setup_override is None or setup_override is False:
-            if agents_override_present:
-                written = maybe_generate_agents_md(
+            if agents_override_present and not agents_disabled:
+                agents_path = maybe_generate_agents_md(
                     console_obj, repo_path, agents_md=agents_override
                 )
-                return [written] if written is not None else []
+                return [agents_path] if agents_path is not None else []
             return []
 
         installed = is_codex_cli_installed()
@@ -56,13 +57,14 @@ def write_project_files(
         hooks_path = save_codex_hooks_config(repo_path)
         console_obj.print(f"  [{OK}]✓[/] Codex hooks registered ({hooks_path})")
         written = [Path(config_path), Path(hooks_path)]
-        agents_path = maybe_generate_agents_md(
-            console_obj,
-            repo_path,
-            agents_md=True if agents_override is None else agents_override,
-        )
-        if agents_path is not None:
-            written.append(agents_path)
+        if not agents_disabled:
+            agents_path = maybe_generate_agents_md(
+                console_obj,
+                repo_path,
+                agents_md=True if agents_override is None else agents_override,
+            )
+            if agents_path is not None:
+                written.append(agents_path)
 
         if not installed:
             console_obj.print(

packages/cli/src/repowise/cli/editor_setup.py

@@ -197,6 +197,48 @@ def resolve_editor_setup_options(
     )
 
 
+def _resolve_configured_project_file_optouts(
+    repo_path: Path,
+    options: EditorSetupOptions,
+) -> EditorSetupOptions:
+    """Merge explicit ``editor_files: <id>: false`` values into *options*.
+
+    The project-file preference belongs to the setup layer, not to an editor
+    integration. Resolving it here gives every write path the same view and
+    lets a newly registered target reuse the descriptor's ``project_file_id``
+    without adding another config reader beside its writer.
+
+    An explicit per-run project-file override remains stronger than the
+    persisted preference. This preserves ``--agents`` / ``--no-agents`` as
+    command-line overrides while still treating a missing key as "let the
+    integration apply its own default" (notably, ``agents_md`` defaults off on
+    the update path).
+    """
+    from repowise.cli.agent_targets.registry import all_targets
+    from repowise.cli.helpers import load_config
+
+    editor_files = load_config(repo_path).get("editor_files")
+    if not isinstance(editor_files, Mapping):
+        return options
+
+    configured_disabled = {
+        target.project_file_id
+        for target in all_targets()
+        if editor_files.get(target.project_file_id) is False
+    }
+    disabled_project_files = (
+        options.disabled_project_files | frozenset(configured_disabled)
+    ) - options.project_file_overrides.keys()
+    if disabled_project_files == options.disabled_project_files:
+        return options
+
+    return EditorSetupOptions(
+        disabled_project_files=frozenset(disabled_project_files),
+        project_file_overrides=dict(options.project_file_overrides),
+        integration_overrides=dict(options.integration_overrides),
+    )
+
+
 def select_agents_interactively(
     console_obj: Any,
     repo_path: Path,
@@ -322,6 +364,8 @@ def write_editor_project_files(
         _persist_project_file_optouts(repo_path, resolved_options)
         return []
 
+    resolved_options = _resolve_configured_project_file_optouts(repo_path, resolved_options)
+
     written: list[Path] = []
     for integration in _resolve_integrations(integrations):
         # ``or []`` rather than a required return: an integration that has
@@ -380,5 +424,6 @@ def refresh_editor_project_files(
     """Refresh editor-managed project files without rewriting common MCP config."""
 
     resolved_options = options or EditorSetupOptions()
+    resolved_options = _resolve_configured_project_file_optouts(repo_path, resolved_options)
     for integration in _resolve_integrations(integrations):
         integration.refresh_project_files(console_obj, repo_path, resolved_options)

tests/unit/cli/test_editor_setup.py

@@ -22,6 +22,7 @@
     get_default_integration_overrides,
     get_default_project_file_overrides,
 )
+from repowise.cli.editor_integrations.vscode import VSCodeSetup
 from repowise.cli.editor_setup import (
     EditorSetupOptions,
     refresh_editor_project_files,
@@ -302,9 +303,7 @@ def test_no_editor_setup_turns_off_every_replacing_surface(monkeypatch, tmp_path
 
     (tmp_path / ".repowise").mkdir()
 
-    offer_distill_rewrite_hook(
-        _silent_console(), [tmp_path], False, yes=True, no_editor_setup=True
-    )
+    offer_distill_rewrite_hook(_silent_console(), [tmp_path], False, yes=True, no_editor_setup=True)
 
     assert _all_same(_hook_verdicts(tmp_path), False)
 
@@ -425,9 +424,7 @@ def _fake(console_obj, choices):
         return answer(choices) if callable(answer) else answer
 
     monkeypatch.setattr(agent_selection, "interactive_agent_select", _fake)
-    options = select_agents_interactively(
-        _silent_console(), tmp_path, EditorSetupOptions(**kwargs)
-    )
+    options = select_agents_interactively(_silent_console(), tmp_path, EditorSetupOptions(**kwargs))
     return options, seen[0]
 
 
@@ -442,9 +439,7 @@ def test_checklist_unticking_an_agent_disables_its_project_file(monkeypatch, tmp
 
 
 def test_checklist_ticking_everything_disables_nothing(monkeypatch, tmp_path) -> None:
-    options, _ = _select(
-        monkeypatch, tmp_path, lambda choices: {choice.id for choice in choices}
-    )
+    options, _ = _select(monkeypatch, tmp_path, lambda choices: {choice.id for choice in choices})
 
     from repowise.cli.editor_integrations.defaults import get_default_editor_integrations
 
@@ -482,9 +477,7 @@ def test_checklist_pre_ticks_an_agent_an_explicit_flag_asked_for(monkeypatch, tm
     Otherwise accepting the checklist would silently undo the flag the user
     passed on the same command line.
     """
-    _, choices = _select(
-        monkeypatch, tmp_path, set(), integration_overrides={"codex": True}
-    )
+    _, choices = _select(monkeypatch, tmp_path, set(), integration_overrides={"codex": True})
 
     codex = next(choice for choice in choices if choice.id == "codex")
     assert codex.enabled is True
@@ -690,6 +683,131 @@ def refresh_project_files(
     assert calls == [("refresh", tmp_path, frozenset({"skip"}))]
 
 
+def test_write_editor_project_files_honors_vscode_config_optout(
+    tmp_path: Path,
+    monkeypatch: Any,
+) -> None:
+    """The init write path resolves an explicit VS Code opt-out centrally."""
+    monkeypatch.delenv("REPOWISE_SKIP_EDITOR_SETUP", raising=False)
+    repowise_dir = tmp_path / ".repowise"
+    repowise_dir.mkdir()
+    (repowise_dir / "config.yaml").write_text(
+        "editor_files:\n  vscode_mcp: false\n",
+        encoding="utf-8",
+    )
+    monkeypatch.setattr(
+        mcp_config,
+        "save_mcp_config",
+        lambda repo_path: repo_path / ".repowise" / "mcp.json",
+    )
+
+    written = write_editor_project_files(
+        _silent_console(),
+        tmp_path,
+        integrations=(VSCodeSetup(),),
+    )
+
+    assert written == []
+    assert not (tmp_path / ".vscode").exists()
+
+
+def test_refresh_editor_project_files_honors_vscode_config_optout(tmp_path: Path) -> None:
+    """The update refresh path applies the same explicit opt-out."""
+    repowise_dir = tmp_path / ".repowise"
+    repowise_dir.mkdir()
+    (repowise_dir / "config.yaml").write_text(
+        "editor_files:\n  vscode_mcp: false\n",
+        encoding="utf-8",
+    )
+
+    refresh_editor_project_files(
+        _silent_console(),
+        tmp_path,
+        integrations=(VSCodeSetup(),),
+    )
+
+    assert not (tmp_path / ".vscode").exists()
+
+
+def test_explicit_project_file_override_wins_over_configured_optout(
+    tmp_path: Path,
+    monkeypatch: Any,
+) -> None:
+    """A per-run override wins even when a disabled set also contains the id."""
+    monkeypatch.delenv("REPOWISE_SKIP_EDITOR_SETUP", raising=False)
+    repowise_dir = tmp_path / ".repowise"
+    repowise_dir.mkdir()
+    (repowise_dir / "config.yaml").write_text(
+        "editor_files:\n  agents_md: false\n",
+        encoding="utf-8",
+    )
+    calls: list[bool | None] = []
+    monkeypatch.setattr(
+        mcp_config,
+        "save_mcp_config",
+        lambda repo_path: repo_path / ".repowise" / "mcp.json",
+    )
+    monkeypatch.setattr(
+        codex_integration,
+        "maybe_generate_agents_md",
+        lambda _console, _repo_path, *, agents_md=None: calls.append(agents_md),
+    )
+
+    write_editor_project_files(
+        _silent_console(),
+        tmp_path,
+        options=EditorSetupOptions(
+            disabled_project_files=frozenset({"agents_md"}),
+            project_file_overrides={"agents_md": True},
+        ),
+        integrations=(CodexSetup(),),
+    )
+
+    assert calls == [True]
+
+
+def test_write_editor_project_files_honors_agents_config_optout_when_codex_enabled(
+    tmp_path: Path,
+    monkeypatch: Any,
+) -> None:
+    """An AGENTS.md opt-out must not disable Codex MCP registration."""
+    monkeypatch.delenv("REPOWISE_SKIP_EDITOR_SETUP", raising=False)
+    repowise_dir = tmp_path / ".repowise"
+    repowise_dir.mkdir()
+    (repowise_dir / "config.yaml").write_text(
+        "editor_files:\n  agents_md: false\n",
+        encoding="utf-8",
+    )
+    monkeypatch.setattr(
+        mcp_config,
+        "save_mcp_config",
+        lambda repo_path: repo_path / ".repowise" / "mcp.json",
+    )
+    calls: list[str] = []
+    monkeypatch.setattr(
+        mcp_config,
+        "save_codex_mcp_config",
+        lambda repo_path: calls.append("mcp") or repo_path / ".codex" / "config.toml",
+    )
+    monkeypatch.setattr(
+        mcp_config,
+        "save_codex_hooks_config",
+        lambda repo_path: calls.append("hooks") or repo_path / ".codex" / "hooks.toml",
+    )
+    monkeypatch.setattr(mcp_config, "is_codex_cli_installed", lambda: False)
+    monkeypatch.setattr(codex_integration, "maybe_generate_agents_md", lambda *args, **kwargs: None)
+
+    written = write_editor_project_files(
+        _silent_console(),
+        tmp_path,
+        options=EditorSetupOptions(integration_overrides={"codex": True}),
+        integrations=(CodexSetup(),),
+    )
+
+    assert calls == ["mcp", "hooks"]
+    assert written == [tmp_path / ".codex" / "config.toml", tmp_path / ".codex" / "hooks.toml"]
+
+
 def _write_settings(path: Path, entry: dict) -> None:
     path.parent.mkdir(parents=True, exist_ok=True)
     path.write_text(json.dumps({"mcpServers": {"repowise": entry}}), encoding="utf-8")