Fix plugin precedence in subordinate profile settings

The profile-settings hook merged a priority-first lookup list with
last-value-wins updates, allowing bundled settings to overwrite community
plugins and higher user/project scopes.

Merge plugin-wide settings, bundled profile, plugin profiles, user profile,
project settings and project profile from low to high priority. Use the
existing stable root-priority sort within each plugin layer, preserving
same-root discovery order, activation scope and cached lookup lists.

Add a failing-before/passing-after regression for both plugin layers,
scoped overrides, fallback, malformed settings and profile/MCP inheritance.
Strengthen metadata override tests with community plugins enabled and
update the agent-init contract.

Validation: 207 focused local tests and 18 precedence tests in the Docker
framework runtime passed. Two isolated fresh-context initialization smoke
checks passed in Docker. git diff --check passed.

extensions/python/agent_init/AGENTS.md

@@ -12,6 +12,7 @@
 
 - Keep initialization idempotent for contexts that may be restored or reloaded.
 - Preserve ordering between initial message creation and profile settings loading.
+- `_15_load_profile_settings.py` merges settings from low to high priority: plugin-wide files, bundled profile, plugin profiles, user profile, project-wide file, then project profile. Each plugin layer applies bundled roots before user roots with a stable root-priority sort, preserving same-root discovery order and cached lookup lists. Global framework and `usr/settings.json` files remain excluded; malformed layers log an error and leave other layers usable. Profile and MCP configuration inherit when not explicitly overridden.
 - Keep a placeholder user turn (`fw.initial_user_message.md`) ahead of the AI greeting (`fw.initial_message.md`) so `output_langchain` never pops the greeting as a leading `AIMessage`; do not remove either prompt without replacing the turn-order guarantee.
 - Minify the initial AI message JSON before storage; preserve raw text as the displayed greeting when JSON parsing fails.
 - `_10_initial_message.py` passes `LLMResult.non_llm()` to `hist_add_ai_response` so the Responses-API state seam runs uniformly; the sentinel carries no `response_id` and marks `mode=""`/`state="off"` so stored metadata does not claim a Responses-API turn.
@@ -24,6 +25,7 @@
 ## Verification
 
 - Smoke-test new chat/context initialization after changes.
+- Run `tests/test_plugin_asset_precedence.py` and `tests/test_subagent_profiles.py` for profile-settings changes.
 
 ## Child DOX Index
 

extensions/python/agent_init/_15_load_profile_settings.py

@@ -1,5 +1,5 @@
 from initialize import initialize_agent
-from helpers import dirty_json, files, subagents, projects
+from helpers import dirty_json, files, subagents, plugins
 from helpers.extension import Extension
 
 
@@ -10,7 +10,25 @@ class LoadProfileSettings(Extension):
         if not self.agent or not self.agent.config.profile:
             return
 
-        config_files = subagents.get_paths(self.agent, "settings.json", include_default=False, include_user=False)
+        profile = self.agent.config.profile
+        scoped_files = subagents.get_paths(
+            self.agent, "settings.json", include_default=False,
+            include_user=False, include_plugins=False,
+        )
+        default_settings = files.get_abs_path(subagents.DEFAULT_AGENTS_DIR, profile, "settings.json")
+        # Merge low-priority layers first, keeping discovery order within plugin roots.
+        config_files = [
+            *sorted(
+                plugins.get_enabled_plugin_paths(self.agent, "settings.json"),
+                key=plugins.get_plugin_root_priority, reverse=True,
+            ),
+            default_settings,
+            *sorted(
+                plugins.get_enabled_plugin_paths(self.agent, "agents", profile, "settings.json"),
+                key=plugins.get_plugin_root_priority, reverse=True,
+            ),
+            *(path for path in reversed(scoped_files) if path != default_settings),
+        ]
         settings_override = {}
         for settings_path in config_files:
             if files.exists(settings_path):

tests/test_plugin_asset_precedence.py

@@ -181,6 +181,7 @@ def test_empty_asset_results_are_cached(plugin_tree, monkeypatch):
     monkeypatch.setattr(plugins, "get_enabled_plugins", unexpected_lookup)
     assert plugins.get_enabled_plugin_paths(None, "missing") == []
 
+
 def test_provider_merges_apply_user_roots_last_and_preserve_same_root_order(plugin_tree):
     roots = [
         plugin_tree("_alpha", bundled=True), plugin_tree("_zulu", bundled=True),
@@ -240,6 +241,7 @@ def test_profile_merges_preserve_root_order_and_higher_scope_overrides(
             state = editor.metadata_state("researcher", editor._EditorContext(project_name or ""))
             assert state["title"]["effective"] == state["context"]["effective"] == title
         else:
+            # The global catalog includes profiles from every project.
             assert subagents.get_all_agents_list() == [{"key": "researcher", "label": title}]
 
     for root in roots:
@@ -254,12 +256,88 @@ def test_profile_merges_preserve_root_order_and_higher_scope_overrides(
     cache.clear("*(plugins)*")
     assert_profile("_zulu")
 
+    for root in roots[2:]:
+        (root / ".toggle-0").unlink()
+    cache.clear("*(plugins)*")
     write_profile(tmp_path / "usr", "User profile")
     assert_profile("User profile")
     write_profile(tmp_path / "usr/projects/demo/.a0proj", "Project profile")
     assert_profile("Project profile", "demo")
 
 
+def test_profile_settings_merge_preserves_root_and_scope_priorities(
+    plugin_tree, tmp_path, monkeypatch
+):
+    from extensions.python.agent_init import _15_load_profile_settings as hook
+
+    roots = [
+        plugin_tree("_alpha", bundled=True), plugin_tree("_zulu", bundled=True),
+        plugin_tree("alpha"), plugin_tree("zulu"),
+    ]
+
+    def write_settings(root, **values):
+        root.mkdir(parents=True, exist_ok=True)
+        path = root / "settings.json"
+        path.write_text(json.dumps(values), encoding="utf-8")
+        return path
+
+    for root in roots:
+        write_settings(root, root_value=root.name, winner=root.name)
+        write_settings(
+            root / "agents/researcher", profile_value=root.name, winner=root.name
+        )
+    write_settings(tmp_path / "agents/researcher", default_only="inherited", winner="default")
+    write_settings(tmp_path, excluded_default=True)
+    write_settings(tmp_path / "usr", excluded_user=True)
+
+    received = []
+    errors = []
+    monkeypatch.setattr(
+        hook, "initialize_agent",
+        lambda override_settings: received.append(override_settings)
+        or SimpleNamespace(profile="default", mcp_servers=""),
+    )
+    agent = SimpleNamespace(
+        config=SimpleNamespace(profile="researcher", mcp_servers="inherited MCP"),
+        context=SimpleNamespace(
+            get_data=lambda *_args: "demo",
+            log=SimpleNamespace(log=lambda **entry: errors.append(entry)),
+        ),
+    )
+
+    def assert_settings(winner, plugin_winner="zulu"):
+        hook.LoadProfileSettings(agent).execute()
+        values = received[-1]
+        assert values["winner"] == winner
+        assert values["root_value"] == values["profile_value"] == plugin_winner
+        assert values["default_only"] == "inherited"
+        assert "excluded_default" not in values and "excluded_user" not in values
+        assert agent.config.profile == "researcher"
+        assert agent.config.mcp_servers == "inherited MCP"
+
+    assert_settings("zulu")
+    assert plugins.get_enabled_plugin_paths(agent, "settings.json") == [
+        str(root / "settings.json") for root in [*roots[2:], *roots[:2]]
+    ]
+    write_settings(tmp_path / "usr/agents/researcher", winner="user")
+    assert_settings("user")
+    project = tmp_path / "usr/projects/demo/.a0proj"
+    write_settings(project, winner="project")
+    assert_settings("project")
+    project_profile = write_settings(project / "agents/researcher", winner="")
+    assert_settings("")
+
+    for root in roots[2:]:
+        (root / ".toggle-0").touch()
+    cache.clear("*(plugins)*")
+    assert_settings("", "_zulu")
+
+    project_profile.write_text("[]", encoding="utf-8")
+    assert_settings("project", "_zulu")
+    assert len(errors) == 1 and errors[0]["type"] == "error"
+    assert str(project_profile) in errors[0]["content"]
+
+
 def test_model_prompt_native_schema_and_dispatch_use_the_same_plugin(
     plugin_tree, monkeypatch, tmp_path
 ):