diff --git a/rust/crates/openjarvis-python/uv.lock b/rust/crates/openjarvis-python/uv.lock
index 38a7ca97..7f3fa09b 100644
--- a/rust/crates/openjarvis-python/uv.lock
+++ b/rust/crates/openjarvis-python/uv.lock
@@ -4,5 +4,5 @@ requires-python = ">=3.10"
 
 [[package]]
 name = "openjarvis-rust"
-version = "1.0.0"
+version = "0.1.0"
 source = { editable = "." }
diff --git a/src/openjarvis/agents/_stubs.py b/src/openjarvis/agents/_stubs.py
index 7ff0fa08..2f8e3011 100644
--- a/src/openjarvis/agents/_stubs.py
+++ b/src/openjarvis/agents/_stubs.py
@@ -223,6 +223,8 @@ class ToolUsingAgent(BaseAgent):
         loop_guard_config: Optional[Any] = None,
         capability_policy: Optional[Any] = None,
         agent_id: Optional[str] = None,
+        interactive: bool = False,
+        confirm_callback: Optional[Any] = None,
     ) -> None:
         super().__init__(
             engine, model, bus=bus,
@@ -236,6 +238,8 @@ class ToolUsingAgent(BaseAgent):
             self._tools, bus=bus,
             capability_policy=capability_policy,
             agent_id=_aid,
+            interactive=interactive,
+            confirm_callback=confirm_callback,
         )
         self._max_turns = max_turns
 
diff --git a/src/openjarvis/agents/monitor_operative.py b/src/openjarvis/agents/monitor_operative.py
index 4cb52576..1f03bae3 100644
--- a/src/openjarvis/agents/monitor_operative.py
+++ b/src/openjarvis/agents/monitor_operative.py
@@ -105,12 +105,15 @@ class MonitorOperativeAgent(ToolUsingAgent):
         operator_id: Optional[str] = None,
         session_store: Optional[Any] = None,
         memory_backend: Optional[Any] = None,
+        interactive: bool = False,
+        confirm_callback=None,
         **kwargs: Any,
     ) -> None:
         super().__init__(
             engine, model, tools=tools, bus=bus,
             max_turns=max_turns, temperature=temperature,
             max_tokens=max_tokens,
+            interactive=interactive, confirm_callback=confirm_callback,
         )
         # Validate strategies
         if memory_extraction not in VALID_MEMORY_EXTRACTION:
diff --git a/src/openjarvis/agents/native_openhands.py b/src/openjarvis/agents/native_openhands.py
index d3d43c82..46570d53 100644
--- a/src/openjarvis/agents/native_openhands.py
+++ b/src/openjarvis/agents/native_openhands.py
@@ -65,11 +65,14 @@ class NativeOpenHandsAgent(ToolUsingAgent):
         max_turns: int = 3,
         temperature: float = 0.7,
         max_tokens: int = 2048,
+        interactive: bool = False,
+        confirm_callback=None,
     ) -> None:
         super().__init__(
             engine, model, tools=tools, bus=bus,
             max_turns=max_turns, temperature=temperature,
             max_tokens=max_tokens,
+            interactive=interactive, confirm_callback=confirm_callback,
         )
 
     @staticmethod
diff --git a/src/openjarvis/agents/native_react.py b/src/openjarvis/agents/native_react.py
index 1c10ddf1..2b14d1c0 100644
--- a/src/openjarvis/agents/native_react.py
+++ b/src/openjarvis/agents/native_react.py
@@ -47,11 +47,14 @@ class NativeReActAgent(ToolUsingAgent):
         max_turns: int = 10,
         temperature: float = 0.7,
         max_tokens: int = 1024,
+        interactive: bool = False,
+        confirm_callback=None,
     ) -> None:
         super().__init__(
             engine, model, tools=tools, bus=bus,
             max_turns=max_turns, temperature=temperature,
             max_tokens=max_tokens,
+            interactive=interactive, confirm_callback=confirm_callback,
         )
 
     def _parse_response(self, text: str) -> dict:
diff --git a/src/openjarvis/agents/operative.py b/src/openjarvis/agents/operative.py
index a98f3f8d..ed56b541 100644
--- a/src/openjarvis/agents/operative.py
+++ b/src/openjarvis/agents/operative.py
@@ -53,12 +53,15 @@ class OperativeAgent(ToolUsingAgent):
         operator_id: Optional[str] = None,
         session_store: Optional[Any] = None,
         memory_backend: Optional[Any] = None,
+        interactive: bool = False,
+        confirm_callback=None,
         **kwargs: Any,
     ) -> None:
         super().__init__(
             engine, model, tools=tools, bus=bus,
             max_turns=max_turns, temperature=temperature,
             max_tokens=max_tokens,
+            interactive=interactive, confirm_callback=confirm_callback,
         )
         self._system_prompt = system_prompt or ""
         self._operator_id = operator_id
diff --git a/src/openjarvis/agents/orchestrator.py b/src/openjarvis/agents/orchestrator.py
index b89a406d..ffbff90e 100644
--- a/src/openjarvis/agents/orchestrator.py
+++ b/src/openjarvis/agents/orchestrator.py
@@ -55,11 +55,14 @@ class OrchestratorAgent(ToolUsingAgent):
         mode: str = "function_calling",
         system_prompt: Optional[str] = None,
         parallel_tools: bool = True,
+        interactive: bool = False,
+        confirm_callback=None,
     ) -> None:
         super().__init__(
             engine, model, tools=tools, bus=bus,
             max_turns=max_turns, temperature=temperature,
             max_tokens=max_tokens,
+            interactive=interactive, confirm_callback=confirm_callback,
         )
         self._mode = mode
         self._system_prompt = system_prompt
diff --git a/src/openjarvis/agents/rlm.py b/src/openjarvis/agents/rlm.py
index c85f5653..26d65bce 100644
--- a/src/openjarvis/agents/rlm.py
+++ b/src/openjarvis/agents/rlm.py
@@ -100,11 +100,14 @@ class RLMAgent(ToolUsingAgent):
         sub_max_tokens: int = 1024,
         max_output_chars: int = 10000,
         system_prompt: Optional[str] = None,
+        interactive: bool = False,
+        confirm_callback=None,
     ) -> None:
         super().__init__(
             engine, model, tools=tools, bus=bus,
             max_turns=max_turns, temperature=temperature,
             max_tokens=max_tokens,
+            interactive=interactive, confirm_callback=confirm_callback,
         )
         # Override executor: RLM only creates one if tools are provided
         if not self._tools:
diff --git a/src/openjarvis/cli/_tool_names.py b/src/openjarvis/cli/_tool_names.py
new file mode 100644
index 00000000..1f093411
--- /dev/null
+++ b/src/openjarvis/cli/_tool_names.py
@@ -0,0 +1,40 @@
+"""Helpers for resolving CLI tool selections."""
+
+from __future__ import annotations
+
+from typing import Any
+
+
+def _normalize_tool_names(value: Any) -> list[str]:
+    """Normalize configured tool names from string or list-like values."""
+    if value is None:
+        return []
+    if isinstance(value, str):
+        return [part.strip() for part in value.split(",") if part.strip()]
+    if isinstance(value, (list, tuple, set)):
+        names = []
+        for item in value:
+            text = str(item).strip()
+            if text:
+                names.append(text)
+        return names
+
+    text = str(value).strip()
+    return [text] if text else []
+
+
+def resolve_tool_names(
+    cli_value: str | None,
+    *configured_values: Any,
+) -> list[str]:
+    """Resolve tool names, preferring explicit CLI values over config fallbacks."""
+    cli_names = _normalize_tool_names(cli_value)
+    if cli_names:
+        return cli_names
+
+    for configured in configured_values:
+        names = _normalize_tool_names(configured)
+        if names:
+            return names
+
+    return []
diff --git a/src/openjarvis/cli/ask.py b/src/openjarvis/cli/ask.py
index b8e11437..faed5a1d 100644
--- a/src/openjarvis/cli/ask.py
+++ b/src/openjarvis/cli/ask.py
@@ -11,6 +11,7 @@ import click
 from rich.console import Console
 from rich.table import Table
 
+from openjarvis.cli._tool_names import resolve_tool_names
 from openjarvis.cli.hints import hint_no_engine
 from openjarvis.core.config import load_config
 from openjarvis.core.events import EventBus, EventType
@@ -126,6 +127,8 @@ def _run_agent(
     if getattr(agent_cls, "accepts_tools", False):
         agent_kwargs["tools"] = tools
         agent_kwargs["max_turns"] = config.agent.max_turns
+        agent_kwargs["interactive"] = True
+        agent_kwargs["confirm_callback"] = lambda prompt: True
 
     agent = agent_cls(engine, model_name, **agent_kwargs)
     ctx = AgentContext()
@@ -388,7 +391,11 @@ def ask(
 
     # Agent mode
     if agent_name is not None:
-        parsed_tools = tool_names.split(",") if tool_names else []
+        parsed_tools = resolve_tool_names(
+            tool_names,
+            getattr(config.tools, "enabled", None),
+            getattr(config.agent, "tools", None),
+        )
         try:
             result = _run_agent(
                 agent_name, query_text, engine, model_name,
diff --git a/src/openjarvis/cli/chat_cmd.py b/src/openjarvis/cli/chat_cmd.py
index be30f6a8..f78f19f2 100644
--- a/src/openjarvis/cli/chat_cmd.py
+++ b/src/openjarvis/cli/chat_cmd.py
@@ -9,6 +9,7 @@ import click
 from rich.console import Console
 from rich.markdown import Markdown
 
+from openjarvis.cli._tool_names import resolve_tool_names
 from openjarvis.core.config import load_config
 from openjarvis.core.types import Message, Role
 
@@ -85,26 +86,41 @@ def chat(
                 agent_cls = AgentRegistry.get(agent_key)
                 kwargs: dict = {"bus": EventBus()}
 
-                if getattr(agent_cls, "accepts_tools", False) and tools:
-                    import openjarvis.tools  # noqa: F401 — trigger registration
-                    from openjarvis.core.registry import ToolRegistry
-                    from openjarvis.tools._stubs import BaseTool
+                if getattr(agent_cls, "accepts_tools", False):
+                    tool_names_list = resolve_tool_names(
+                        tools,
+                        getattr(config.tools, "enabled", None),
+                        getattr(config.agent, "tools", None),
+                    )
+                    if tool_names_list:
+                        import openjarvis.tools  # noqa: F401 — trigger registration
+                        from openjarvis.core.registry import ToolRegistry
+                        from openjarvis.tools._stubs import BaseTool
 
-                    tool_instances = []
-                    for tname in tools.split(","):
-                        tname = tname.strip()
-                        if ToolRegistry.contains(tname):
-                            tcls = ToolRegistry.get(tname)
-                            if isinstance(tcls, type) and issubclass(
-                                tcls, BaseTool
-                            ):
-                                tool_instances.append(tcls())
-                            elif isinstance(tcls, BaseTool):
-                                tool_instances.append(tcls)
-                    if tool_instances:
-                        kwargs["tools"] = tool_instances
+                        tool_instances = []
+                        for tname in tool_names_list:
+                            if ToolRegistry.contains(tname):
+                                tcls = ToolRegistry.get(tname)
+                                if isinstance(tcls, type) and issubclass(
+                                    tcls, BaseTool
+                                ):
+                                    tool_instances.append(tcls())
+                                elif isinstance(tcls, BaseTool):
+                                    tool_instances.append(tcls)
+                        if tool_instances:
+                            kwargs["tools"] = tool_instances
                     kwargs["max_turns"] = config.agent.max_turns
 
+                    def _confirm(prompt: str) -> bool:
+                        console.print(
+                            f"[yellow]Confirm:[/yellow] {prompt} [y/N] ",
+                            end="",
+                        )
+                        ans = input().strip().lower()
+                        return ans in ("y", "yes")
+
+                    kwargs["interactive"] = True
+                    kwargs["confirm_callback"] = _confirm
                 agent = agent_cls(engine, model, **kwargs)
         except Exception as exc:
             console.print(f"[yellow]Agent '{agent_key}' failed: {exc}[/yellow]")
diff --git a/src/openjarvis/tools/__init__.py b/src/openjarvis/tools/__init__.py
index 5efb36ab..b95c9090 100644
--- a/src/openjarvis/tools/__init__.py
+++ b/src/openjarvis/tools/__init__.py
@@ -72,4 +72,9 @@ try:
 except ImportError:
     pass
 
+try:
+    import openjarvis.tools.shell_exec  # noqa: F401
+except ImportError:
+    pass
+
 __all__ = ["BaseTool", "ToolExecutor", "ToolSpec"]
diff --git a/tests/agents/test_base_agent.py b/tests/agents/test_base_agent.py
index a03197d2..b1c0313e 100644
--- a/tests/agents/test_base_agent.py
+++ b/tests/agents/test_base_agent.py
@@ -11,7 +11,7 @@ from openjarvis.agents._stubs import (
     ToolUsingAgent,
 )
 from openjarvis.core.events import EventBus, EventType
-from openjarvis.core.types import Conversation, Message, Role, ToolResult
+from openjarvis.core.types import Conversation, Message, Role, ToolCall, ToolResult
 from openjarvis.tools._stubs import BaseTool, ToolSpec
 
 # ---------------------------------------------------------------------------
@@ -48,6 +48,22 @@ class _DummyTool(BaseTool):
         return ToolResult(tool_name="dummy", content="ok", success=True)
 
 
+class _ConfirmTool(BaseTool):
+    tool_id = "confirm"
+
+    @property
+    def spec(self) -> ToolSpec:
+        return ToolSpec(
+            name="confirm",
+            description="Confirmation-required tool.",
+            parameters={"type": "object", "properties": {}},
+            requires_confirmation=True,
+        )
+
+    def execute(self, **params) -> ToolResult:
+        return ToolResult(tool_name="confirm", content="confirmed", success=True)
+
+
 # ---------------------------------------------------------------------------
 # BaseAgent tests
 # ---------------------------------------------------------------------------
@@ -269,3 +285,21 @@ class TestToolUsingAgent:
         agent._emit_turn_start("hi")
         events = [e for e in bus.history if e.event_type == EventType.AGENT_TURN_START]
         assert len(events) == 1
+
+    def test_propagates_confirmation_settings_to_executor(self):
+        engine = MagicMock()
+        confirm = MagicMock(return_value=True)
+        agent = _ConcreteToolAgent(
+            engine,
+            "m",
+            tools=[_ConfirmTool()],
+            interactive=True,
+            confirm_callback=confirm,
+        )
+
+        result = agent._executor.execute(
+            ToolCall(id="1", name="confirm", arguments="{}")
+        )
+
+        assert result.success is True
+        confirm.assert_called_once()
diff --git a/tests/cli/test_ask_agent.py b/tests/cli/test_ask_agent.py
index e4a1a3ad..577aa499 100644
--- a/tests/cli/test_ask_agent.py
+++ b/tests/cli/test_ask_agent.py
@@ -3,12 +3,16 @@
 from __future__ import annotations
 
 import importlib
+from dataclasses import dataclass
 from unittest.mock import MagicMock, patch
 
 import pytest
 from click.testing import CliRunner
 
+from openjarvis.agents._stubs import AgentContext, AgentResult, ToolUsingAgent
 from openjarvis.cli import cli
+from openjarvis.core.types import ToolCall, ToolResult
+from openjarvis.tools._stubs import BaseTool, ToolSpec
 
 _ask_mod = importlib.import_module("openjarvis.cli.ask")
 
@@ -62,6 +66,72 @@ def _register_tools():
             ToolRegistry.register_value(name, cls)
 
 
+class _DangerousTool(BaseTool):
+    tool_id = "dangerous"
+
+    @property
+    def spec(self) -> ToolSpec:
+        return ToolSpec(
+            name="dangerous",
+            description="Confirmation-gated test tool.",
+            requires_confirmation=True,
+        )
+
+    def execute(self, **params) -> ToolResult:
+        return ToolResult(
+            tool_name="dangerous",
+            content="executed!",
+            success=True,
+        )
+
+
+class _ConfirmingAgent(ToolUsingAgent):
+    agent_id = "confirming_agent"
+
+    def run(self, input, context: AgentContext | None = None, **kwargs):
+        result = self._executor.execute(
+            ToolCall(id="confirm", name="dangerous", arguments="{}")
+        )
+        return AgentResult(
+            content=result.content,
+            tool_results=[result],
+            turns=1,
+        )
+
+
+@dataclass
+class _EngineSetup:
+    engine: MagicMock
+    config: object
+
+
+@pytest.fixture
+def agent_setup():
+    from openjarvis.core.config import JarvisConfig
+    from openjarvis.core.registry import AgentRegistry, ToolRegistry
+
+    engine = _mock_engine("unused")
+    config = JarvisConfig()
+    config.intelligence.default_model = "test-model"
+    config.agent.max_turns = 3
+
+    AgentRegistry.register_value("confirming_agent", _ConfirmingAgent)
+    ToolRegistry.register_value("dangerous", _DangerousTool)
+
+    with (
+        patch.object(_ask_mod, "load_config", return_value=config),
+        patch.object(_ask_mod, "get_engine", return_value=("mock", engine)),
+        patch.object(_ask_mod, "discover_engines", return_value=[("mock", engine)]),
+        patch.object(
+            _ask_mod, "discover_models",
+            return_value={"mock": ["test-model"]},
+        ),
+        patch.object(_ask_mod, "register_builtin_models"),
+        patch.object(_ask_mod, "merge_discovered_models"),
+    ):
+        yield _EngineSetup(engine=engine, config=config)
+
+
 @pytest.fixture
 def runner():
     return CliRunner()
@@ -151,6 +221,32 @@ class TestAskAgentOption:
         )
         assert result.exit_code == 0
 
+    @pytest.mark.parametrize(
+        ("tools_enabled", "agent_tools"),
+        [
+            (["dangerous"], ""),
+            ("dangerous", ""),
+            ("", "dangerous"),
+        ],
+    )
+    def test_agent_uses_configured_tools_by_default(
+        self,
+        runner,
+        agent_setup,
+        tools_enabled,
+        agent_tools,
+    ):
+        agent_setup.config.tools.enabled = tools_enabled
+        agent_setup.config.agent.tools = agent_tools
+
+        result = runner.invoke(
+            cli, ["ask", "--agent", "confirming_agent", "Hello"],
+        )
+
+        assert result.exit_code == 0
+        assert "executed!" in result.output
+        agent_setup.engine.generate.assert_not_called()
+
 
 class TestBuildTools:
     def test_build_calculator(self, mock_setup):
diff --git a/tests/cli/test_chat_cmd.py b/tests/cli/test_chat_cmd.py
index a7be1f0d..18adc151 100644
--- a/tests/cli/test_chat_cmd.py
+++ b/tests/cli/test_chat_cmd.py
@@ -3,10 +3,57 @@
 from __future__ import annotations
 
 from unittest import mock
+from unittest.mock import MagicMock, patch
 
 from click.testing import CliRunner
 
+from openjarvis.agents._stubs import (
+    AgentContext,
+    AgentResult,
+    BaseAgent,
+    ToolUsingAgent,
+)
 from openjarvis.cli.chat_cmd import _read_input, chat
+from openjarvis.core.config import JarvisConfig
+from openjarvis.core.registry import AgentRegistry, ToolRegistry
+from openjarvis.core.types import ToolCall, ToolResult
+from openjarvis.tools._stubs import BaseTool, ToolSpec
+
+
+class _SimpleChatAgent(BaseAgent):
+    agent_id = "simple_chat_agent"
+
+    def run(self, input, context: AgentContext | None = None, **kwargs):
+        return AgentResult(content="simple ok", turns=1)
+
+
+class _DangerousChatTool(BaseTool):
+    tool_id = "dangerous_chat"
+
+    @property
+    def spec(self) -> ToolSpec:
+        return ToolSpec(
+            name="dangerous_chat",
+            description="Confirmation-gated chat tool.",
+            requires_confirmation=True,
+        )
+
+    def execute(self, **params) -> ToolResult:
+        return ToolResult(
+            tool_name="dangerous_chat",
+            content="chat executed!",
+            success=True,
+        )
+
+
+class _ToolChatAgent(ToolUsingAgent):
+    agent_id = "tool_chat_agent"
+
+    def run(self, input, context: AgentContext | None = None, **kwargs):
+        result = self._executor.execute(
+            ToolCall(id="chat", name="dangerous_chat", arguments="{}")
+        )
+        return AgentResult(content=result.content, tool_results=[result], turns=1)
 
 
 class TestChatCommand:
@@ -46,3 +93,55 @@ class TestReadInput:
     def test_read_input_normal(self) -> None:
         with mock.patch("builtins.input", return_value="hello"):
             assert _read_input() == "hello"
+
+
+class TestChatAgents:
+    def test_simple_agent_does_not_receive_tool_only_kwargs(self) -> None:
+        engine = MagicMock()
+        engine.engine_id = "mock"
+        engine.generate.return_value = {"content": "engine fallback"}
+        config = JarvisConfig()
+        config.intelligence.default_model = "test-model"
+
+        AgentRegistry.register_value("simple_chat_agent", _SimpleChatAgent)
+
+        with (
+            patch("openjarvis.cli.chat_cmd.load_config", return_value=config),
+            patch("openjarvis.engine.get_engine", return_value=("mock", engine)),
+            patch("openjarvis.intelligence.register_builtin_models"),
+        ):
+            result = CliRunner().invoke(
+                chat,
+                ["--agent", "simple_chat_agent", "--model", "test-model"],
+                input="hello\n/quit\n",
+            )
+
+        assert result.exit_code == 0
+        assert "simple ok" in result.output
+        assert "failed" not in result.output.lower()
+
+    def test_tool_agent_uses_legacy_agent_tools_and_prompts_confirmation(self) -> None:
+        engine = MagicMock()
+        engine.engine_id = "mock"
+        config = JarvisConfig()
+        config.intelligence.default_model = "test-model"
+        config.agent.tools = "dangerous_chat"
+        config.agent.max_turns = 3
+
+        AgentRegistry.register_value("tool_chat_agent", _ToolChatAgent)
+        ToolRegistry.register_value("dangerous_chat", _DangerousChatTool)
+
+        with (
+            patch("openjarvis.cli.chat_cmd.load_config", return_value=config),
+            patch("openjarvis.engine.get_engine", return_value=("mock", engine)),
+            patch("openjarvis.intelligence.register_builtin_models"),
+        ):
+            result = CliRunner().invoke(
+                chat,
+                ["--agent", "tool_chat_agent", "--model", "test-model"],
+                input="run tool\ny\n/quit\n",
+            )
+
+        assert result.exit_code == 0
+        assert "Confirm:" in result.output
+        assert "chat executed!" in result.output
diff --git a/tests/tools/test_shell_exec.py b/tests/tools/test_shell_exec.py
index f68c1e3b..50999e57 100644
--- a/tests/tools/test_shell_exec.py
+++ b/tests/tools/test_shell_exec.py
@@ -7,7 +7,9 @@ the Rust output format correctly:
 
 from __future__ import annotations
 
+import importlib
 import os
+import sys
 from unittest.mock import MagicMock, patch
 
 import pytest
@@ -35,6 +37,15 @@ def _make_mock_rust(side_effect=None, return_value=None):
 
 
 class TestShellExecTool:
+    def test_registered_via_tools_package_import(self):
+        import openjarvis.tools as tools_pkg
+        from openjarvis.core.registry import ToolRegistry
+
+        sys.modules.pop("openjarvis.tools.shell_exec", None)
+        importlib.reload(tools_pkg)
+
+        assert ToolRegistry.contains("shell_exec")
+
     def test_spec(self):
         tool = ShellExecTool()
         assert tool.spec.name == "shell_exec"
diff --git a/uv.lock b/uv.lock
index 8a54b536..f05db6d8 100644
--- a/uv.lock
+++ b/uv.lock
@@ -197,6 +197,21 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/fb/76/641ae371508676492379f16e2fa48f4e2c11741bd63c48be4b12a6b09cba/aiosignal-1.4.0-py3-none-any.whl", hash = "sha256:053243f8b92b990551949e63930a839ff0cf0b0ebbe0597b0f3fb19e1a0fe82e", size = 7490, upload-time = "2025-07-03T22:54:42.156Z" },
 ]
 
+[[package]]
+name = "alembic"
+version = "1.18.4"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "mako" },
+    { name = "sqlalchemy" },
+    { name = "tomli", marker = "python_full_version < '3.11'" },
+    { name = "typing-extensions" },
+]
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+learning-dspy = [
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+]
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 media = [
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