Add Phase 6: write tools, shell, and edit tools with reasoning-only fix

Implement 6 new agent tools — write_file, make_dir, delete_file,
str_replace, patch_apply, run_command — bringing the agent from
read-only observer to active code modifier. All write/shell operations
are gated through the existing permissions service.

Also fix a bug where qwen3.5 thinking mode produces reasoning tokens
but no content after tool results, causing the agent to silently exit.
The loop now detects reasoning-only responses, retries twice, then
injects a nudge message to break the model out of its thinking loop.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

tests/unit/test_shell.py

@@ -0,0 +1,95 @@
+"""Tests for the run_command shell tool (Phase 6)."""
+
+import subprocess
+from pathlib import Path
+from unittest.mock import patch as mock_patch
+
+import pytest
+
+from app.models.config import AppConfig, load_config
+from app.models.tool_call import ToolResultStatus
+from app.tools.shell import RunCommandTool
+
+
+@pytest.fixture
+def config() -> AppConfig:
+    return load_config()
+
+
+@pytest.fixture
+def tmp_workspace(tmp_path: Path, config: AppConfig) -> tuple[Path, AppConfig]:
+    """Create a temporary workspace for shell tests."""
+    config.agent.workspace_root = tmp_path
+    return tmp_path, config
+
+
+class TestRunCommandTool:
+    def test_allowed_command_runs(self, tmp_workspace: tuple[Path, AppConfig]) -> None:
+        ws, cfg = tmp_workspace
+        tool = RunCommandTool(ws, cfg)
+        result = tool.run("tc-1", {"command": "echo hello"})
+        assert result.status == ToolResultStatus.SUCCESS
+        assert "hello" in result.output
+
+    def test_denied_command_blocked(self, tmp_workspace: tuple[Path, AppConfig]) -> None:
+        ws, cfg = tmp_workspace
+        tool = RunCommandTool(ws, cfg)
+        result = tool.run("tc-2", {"command": "sudo rm -rf /"})
+        assert result.status == ToolResultStatus.ERROR
+        assert "denied" in (result.error or "").lower()
+
+    def test_disallowed_command_blocked(self, tmp_workspace: tuple[Path, AppConfig]) -> None:
+        ws, cfg = tmp_workspace
+        tool = RunCommandTool(ws, cfg)
+        result = tool.run("tc-3", {"command": "curl http://example.com"})
+        assert result.status == ToolResultStatus.ERROR
+        assert "denied" in (result.error or "").lower()
+
+    def test_unlisted_command_blocked(self, tmp_workspace: tuple[Path, AppConfig]) -> None:
+        ws, cfg = tmp_workspace
+        tool = RunCommandTool(ws, cfg)
+        result = tool.run("tc-4", {"command": "nc -l 1234"})
+        assert result.status == ToolResultStatus.ERROR
+        assert "not in the allowed" in (result.error or "").lower()
+
+    def test_nonzero_exit_code_reported(self, tmp_workspace: tuple[Path, AppConfig]) -> None:
+        ws, cfg = tmp_workspace
+        tool = RunCommandTool(ws, cfg)
+        # ls on a nonexistent path returns non-zero
+        result = tool.run("tc-5", {"command": "ls /nonexistent_path_xyz"})
+        assert result.status == ToolResultStatus.SUCCESS
+        assert "Exit code:" in result.output
+
+    def test_timeout(self, tmp_workspace: tuple[Path, AppConfig]) -> None:
+        ws, cfg = tmp_workspace
+        tool = RunCommandTool(ws, cfg)
+        with mock_patch(
+            "app.tools.shell.subprocess.run",
+            side_effect=subprocess.TimeoutExpired("cmd", 1),
+        ):
+            result = tool.run("tc-6", {"command": "echo test", "timeout": 1})
+        assert result.status == ToolResultStatus.ERROR
+        assert "timed out" in (result.error or "").lower()
+
+    def test_empty_command(self, tmp_workspace: tuple[Path, AppConfig]) -> None:
+        ws, cfg = tmp_workspace
+        tool = RunCommandTool(ws, cfg)
+        result = tool.run("tc-7", {"command": ""})
+        assert result.status == ToolResultStatus.ERROR
+        assert "empty" in (result.error or "").lower()
+
+    def test_custom_timeout(self, tmp_workspace: tuple[Path, AppConfig]) -> None:
+        ws, cfg = tmp_workspace
+        tool = RunCommandTool(ws, cfg)
+        result = tool.run("tc-8", {"command": "echo fast", "timeout": 60})
+        assert result.status == ToolResultStatus.SUCCESS
+        assert "fast" in result.output
+
+    def test_runs_in_workspace_dir(self, tmp_workspace: tuple[Path, AppConfig]) -> None:
+        ws, cfg = tmp_workspace
+        # Create a file in the workspace to verify cwd
+        (ws / "marker.txt").write_text("found")
+        tool = RunCommandTool(ws, cfg)
+        result = tool.run("tc-9", {"command": "cat marker.txt"})
+        assert result.status == ToolResultStatus.SUCCESS
+        assert "found" in result.output