Fix native workflow completion and runtime behavior

apodex/agent_tools.py

@@ -284,6 +284,21 @@ def localize_path_args(name: str, args: dict, cwd: str) -> dict | None:
         except Exception:
             continue
         if not (rel == ".." or rel.startswith(".." + os.sep)):
+            # Native workflow mode deliberately separates the user's project
+            # (cwd) from its run-private execution workspace. The workflow
+            # read_file resolves relative paths in that private workspace, so
+            # converting a correct absolute project path to "README.md" would
+            # make it read the wrong filesystem location.
+            runtime_workspace = os.environ.get(
+                "FRONTIER_AGENT_WORKSPACE_DIR", ""
+            ).strip()
+            if name == "read_file" and runtime_workspace:
+                try:
+                    workspace_real = os.path.realpath(runtime_workspace)
+                except Exception:
+                    workspace_real = ""
+                if workspace_real and workspace_real != cwd_real:
+                    return None
             new = dict(args)
             new[key] = rel or "."
             return new

apodex/task_runner.py

@@ -93,6 +93,17 @@ def _is_complete_run(
     # phase hit its soft deadline. Its explicit complete status is authoritative.
     if answer_status == "complete" and answer_source == "reporter_llm":
         return True
+    # Main-agent workflows may finish with a plain-text assistant turn, which
+    # the loop records as ``no_tool``. Once the workflow has explicitly marked
+    # that agent-produced answer complete, treat that terminal as successful.
+    # Keep this narrower than accepting workflow ``no_tool`` in general: an
+    # exhausted no-tool nudge budget can also use the same stop reason.
+    if (
+        stopped_by == _NO_TOOL_STOP
+        and answer_status == "complete"
+        and answer_source == "agent"
+    ):
+        return True
     if no_tool_is_complete and stopped_by == _NO_TOOL_STOP:
         return True
     return stopped_by in _COMPLETE_TOP_LEVEL_STOPS
@@ -565,18 +576,28 @@ async def _run_native_workflow(self, task: str, profile: Any) -> None:
             answer_status=str(state.get("answer_status") or ""),
             answer_source=str(state.get("final_answer_source") or ""),
         )
+        turns_used = (
+            int(state.get("turns_used") or 0)
+            if "turns_used" in state
+            else len(state.get("react_steps") or [])
+        )
+        tool_calls_count = (
+            int(state.get("tool_calls_count") or 0)
+            if "tool_calls_count" in state
+            else 0
+        )
         if complete:
             self.r.final(
                 final,
-                turns=len(state.get("react_steps") or []),
-                tool_calls=0,
+                turns=turns_used,
+                tool_calls=tool_calls_count,
                 stopped_by=stopped_by,
             )
         else:
             self._show_incomplete_run(
                 final,
-                turns=len(state.get("react_steps") or []),
-                tool_calls=0,
+                turns=turns_used,
+                tool_calls=tool_calls_count,
                 stopped_by=stopped_by,
             )
         await self._render_changed_files()

apodex/tests/test_features.py

@@ -284,6 +284,27 @@ def test_localize_absolute_path_inside_cwd(tmp_path):
     assert out is not None and out["path"] == "sub/f.py"
 
 
+def test_read_file_keeps_project_absolute_path_with_split_runtime_workspace(
+    tmp_path, monkeypatch,
+):
+    project = tmp_path / "project"
+    runtime_workspace = tmp_path / "private-workspace"
+    project.mkdir()
+    runtime_workspace.mkdir()
+    target = project / "README.md"
+    target.write_text("# project\n")
+
+    monkeypatch.setenv(
+        "FRONTIER_AGENT_WORKSPACE_DIR", str(runtime_workspace),
+    )
+
+    out = localize_path_args(
+        "read_file", {"path": str(target)}, str(project),
+    )
+
+    assert out is None
+
+
 def test_localize_preserves_absolute_task_input_path(tmp_path, monkeypatch):
     inputs = tmp_path / ".apodex" / "inputs" / "run"
     inputs.mkdir(parents=True)
@@ -931,6 +952,8 @@ def test_native_workflow_no_tool_stop_is_not_reported_as_delivery(
     assert "no_tool" in out
     assert "partial output was not saved as a final report" in out
     assert "Final report" not in out
+    assert "turns=12" in out
+    assert "tools=0" in out
 
 
 def test_generic_loop_no_tool_stop_is_a_normal_finish():
@@ -942,6 +965,33 @@ def test_generic_loop_no_tool_stop_is_a_normal_finish():
     assert _is_complete_run("max_turns", no_tool_is_complete=True) is False
 
 
+def test_workflow_complete_agent_no_tool_is_a_normal_finish():
+    """A workflow-certified agent answer may terminate via a tool-free turn."""
+    from apodex.task_runner import _is_complete_run
+
+    assert _is_complete_run(
+        "no_tool",
+        answer_status="complete",
+        answer_source="agent",
+    ) is True
+
+    # Do not broaden workflow no_tool into an unconditional success signal.
+    assert _is_complete_run(
+        "no_tool",
+        answer_status="best_effort",
+        answer_source="agent",
+    ) is False
+    assert _is_complete_run(
+        "no_tool",
+        answer_source="agent",
+    ) is False
+    assert _is_complete_run(
+        "max_turns",
+        answer_status="complete",
+        answer_source="agent",
+    ) is False
+
+
 async def _drive_workflow(session, profile, follow_up):
     """Run one native workflow with ``run_task`` stubbed to record follow-ups."""
     session.run_task = follow_up  # type: ignore[method-assign]
@@ -1528,3 +1578,20 @@ def test_download_file_target_is_the_resolved_destination(monkeypatch, tmp_path)
     assert named.startswith(str(tmp_path / "downloads" / "p.pdf"))
     assert "/elsewhere/" not in named           # the requested directory is ignored
     assert "renamed" in named                   # collisions rename it
+
+
+def test_native_workflow_uses_authoritative_loop_telemetry(
+    tmp_path, monkeypatch, capsys,
+):
+    _run_workflow_returning({
+        "final_answer": "done",
+        "answer_status": "complete",
+        "final_answer_source": "agent",
+        "stopped_by": "no_tool",
+        "react_steps": [{}] * 7,
+        "turns_used": 8,
+        "tool_calls_count": 7,
+    }, tmp_path, monkeypatch)
+
+    out = capsys.readouterr().out
+    assert "turns=8 · tools=7 · no_tool" in out

apodex/tests/test_native.py

@@ -60,6 +60,66 @@ def test_native_strategy_is_explicitly_not_os_isolated() -> None:
     assert "not an OS sandbox" in strategy.describe()
 
 
+def test_nonroot_native_current_sandbox_skips_tool_user_warning(
+    tmp_path, monkeypatch, caplog,
+) -> None:
+    from plugins.tools import _sandbox as tool_sandbox
+
+    monkeypatch.setenv("APODEX_IN_NATIVE", "1")
+    monkeypatch.delenv("FRONTIER_AGENT_REQUIRE_TOOL_USER", raising=False)
+    monkeypatch.setattr(tool_sandbox.os, "geteuid", lambda: 1000)
+    monkeypatch.setattr(
+        tool_sandbox, "container_uses_inner_bwrap", lambda: False,
+    )
+
+    def unexpected_identity_lookup():
+        raise AssertionError(
+            "ordinary non-root native mode must not request a tool-user identity"
+        )
+
+    monkeypatch.setattr(
+        tool_sandbox, "tool_identity", unexpected_identity_lookup,
+    )
+
+    current = tool_sandbox.CurrentSandbox(tmp_path)
+
+    assert current.commands._identity is None
+    assert "Tool-user isolation inactive" not in caplog.text
+    assert "own uid" not in caplog.text
+
+
+def test_strict_nonroot_native_still_requires_tool_identity(
+    tmp_path, monkeypatch,
+) -> None:
+    from plugins.tools import _sandbox as tool_sandbox
+
+    monkeypatch.setenv("APODEX_IN_NATIVE", "1")
+    monkeypatch.setenv("FRONTIER_AGENT_REQUIRE_TOOL_USER", "1")
+    monkeypatch.setattr(tool_sandbox.os, "geteuid", lambda: 1000)
+    monkeypatch.setattr(
+        tool_sandbox, "container_uses_inner_bwrap", lambda: False,
+    )
+
+    calls = []
+
+    def required_identity():
+        calls.append(True)
+        raise tool_sandbox.SandboxUnavailableError(
+            "strict tool-user requirement exercised"
+        )
+
+    monkeypatch.setattr(tool_sandbox, "tool_identity", required_identity)
+
+    try:
+        tool_sandbox.CurrentSandbox(tmp_path)
+    except tool_sandbox.SandboxUnavailableError as exc:
+        assert "strict tool-user requirement exercised" in str(exc)
+    else:
+        raise AssertionError("strict native mode unexpectedly bypassed tool_identity")
+
+    assert calls == [True]
+
+
 def test_native_runtime_resolves_canonical_mount_aliases(
     tmp_path, monkeypatch,
 ) -> None:

plugins/tools/_sandbox.py

@@ -1428,6 +1428,23 @@ def _check_ulimit_below_cgroup(mem_mb: int) -> None:
         )
 
 
+def _native_same_uid_is_expected() -> bool:
+    """True when local native execution intentionally uses the harness uid.
+
+    Native mode is explicitly not an OS sandbox: a normal non-root invocation
+    runs approved model commands with the current user's permissions.  Do not
+    route that expected case through the container/service tool-user warning
+    path.  Root-native and explicitly strict runs still attempt the dedicated
+    tool identity.
+    """
+    return (
+        os.environ.get("APODEX_IN_NATIVE", "").strip() == "1"
+        and os.name == "posix"
+        and os.geteuid() != 0
+        and not _require_tool_user()
+    )
+
+
 class _CurrentCommands:
     """Command executor for an existing checkout in the current process.
 
@@ -1438,8 +1455,10 @@ class _CurrentCommands:
 
     def __init__(self, workdir: str, *, private_tmp: bool = False) -> None:
         self._workdir = workdir
-        self._identity = tool_identity()
         native = os.environ.get("APODEX_IN_NATIVE", "").strip() == "1"
+        self._identity = (
+            None if _native_same_uid_is_expected() else tool_identity()
+        )
         self._runtime_home = (
             os.environ.get("HOME", "").strip() or workdir
             if native else workdir
@@ -2023,13 +2042,15 @@ def __init__(self, workdir: str | Path, *, private_tmp: bool = False) -> None:
             self.commands = self._inner.commands
             self.files = self._inner.files
         else:
-            identity = tool_identity()
+            same_uid_expected = _native_same_uid_is_expected()
+            identity = None if same_uid_expected else tool_identity()
             if identity is None:
-                logger.warning(
-                    "CurrentSandbox running model commands with the harness's "
-                    "own uid: the child environment is scrubbed, but "
-                    "/proc/<harness-pid>/environ remains readable"
-                )
+                if not same_uid_expected:
+                    logger.warning(
+                        "CurrentSandbox running model commands with the harness's "
+                        "own uid: the child environment is scrubbed, but "
+                        "/proc/<harness-pid>/environ remains readable"
+                    )
             else:
                 _, outputs_dir, inputs_dir = resolve_mount_dirs()
                 _prepare_tool_writable(self._workdir, outputs_dir)

workflows/stateful_react_agent/nodes/main_agent.py

@@ -1162,6 +1162,10 @@ async def react_agent_node(state: dict[str, Any], ctx: NodeContext) -> dict[str,
             steps=result.metadata.get("react_steps", []),
         ),
         "react_steps": result.metadata.get("react_steps", []),
+        # Authoritative loop telemetry. ``react_steps`` counts tool results,
+        # not LLM turns, so it cannot substitute for either counter.
+        "turns_used": result.turns_used,
+        "tool_calls_count": result.tool_calls_count,
         "language": answer_language,
         # Keep the user-facing answer non-empty while preserving the old
         # machine-readable infra/eval failure signal out of band.