EvoScientist 0.0.1.dev2__py3-none-any.whl → 0.0.1.dev4__py3-none-any.whl

EvoScientist/cli.py

@@ -10,1370 +10,216 @@ Features:
 - Response panel (green) - shows final response
 - Thread ID support for multi-turn conversations
 - Interactive mode with prompt_toolkit
+- Configuration management (onboard, config commands)
 """
 
-import argparse
-import asyncio
+import logging
 import os
 import sys
 import uuid
 from datetime import datetime
-from typing import Any, AsyncIterator
+from typing import Any, Optional
 
-from dotenv import load_dotenv  # type: ignore[import-untyped]
+import typer  # type: ignore[import-untyped]
 from prompt_toolkit import PromptSession  # type: ignore[import-untyped]
 from prompt_toolkit.history import FileHistory  # type: ignore[import-untyped]
 from prompt_toolkit.auto_suggest import AutoSuggestFromHistory  # type: ignore[import-untyped]
 from prompt_toolkit.formatted_text import HTML  # type: ignore[import-untyped]
-from rich.console import Console, Group  # type: ignore[import-untyped]
-from rich.panel import Panel  # type: ignore[import-untyped]
-from rich.markdown import Markdown  # type: ignore[import-untyped]
-from rich.live import Live  # type: ignore[import-untyped]
 from rich.text import Text  # type: ignore[import-untyped]
-from rich.spinner import Spinner  # type: ignore[import-untyped]
-from langchain_core.messages import AIMessage, AIMessageChunk  # type: ignore[import-untyped]
+from rich.table import Table  # type: ignore[import-untyped]
 
-from .stream import (
-    StreamEventEmitter,
-    ToolCallTracker,
-    ToolResultFormatter,
-    DisplayLimits,
-    ToolStatus,
-    format_tool_compact,
-    is_success,
-)
+# Backward-compat re-exports (tests import these from EvoScientist.cli)
+from .stream.state import SubAgentState, StreamState, _parse_todo_items, _build_todo_stats  # noqa: F401
+from .stream.display import console, _run_streaming
+from .paths import ensure_dirs, new_run_dir, default_workspace_dir
 
-load_dotenv(override=True)
-
-console = Console(
-    legacy_windows=(sys.platform == 'win32'),
-    no_color=os.getenv('NO_COLOR') is not None,
-)
-
-formatter = ToolResultFormatter()
-
-
-# =============================================================================
-# Stream event generator
-# =============================================================================
-
-async def stream_agent_events(agent: Any, message: str, thread_id: str) -> AsyncIterator[dict]:
-    """Stream events from the agent graph using async iteration.
-
-    Uses agent.astream() with subgraphs=True to see sub-agent activity.
-
-    Args:
-        agent: Compiled state graph from create_deep_agent()
-        message: User message
-        thread_id: Thread ID for conversation persistence
-
-    Yields:
-        Event dicts: thinking, text, tool_call, tool_result,
-                     subagent_start, subagent_tool_call, subagent_tool_result, subagent_end,
-                     done, error
-    """
-    config = {"configurable": {"thread_id": thread_id}}
-    emitter = StreamEventEmitter()
-    main_tracker = ToolCallTracker()
-    full_response = ""
-
-    # Track sub-agent names
-    _key_to_name: dict[str, str] = {}     # subagent_key → display name (cache)
-    _announced_names: list[str] = []       # ordered queue of announced task names
-    _assigned_names: set[str] = set()      # names already assigned to a namespace
-    _announced_task_ids: list[str] = []     # ordered task tool_call_ids
-    _task_id_to_name: dict[str, str] = {}  # tool_call_id → sub-agent name
-    _subagent_trackers: dict[str, ToolCallTracker] = {}  # namespace_key → tracker
-
-    def _register_task_tool_call(tc_data: dict) -> str | None:
-        """Register or update a task tool call, return subagent name if started/updated."""
-        tool_id = tc_data.get("id", "")
-        if not tool_id:
-            return None
-        args = tc_data.get("args", {}) or {}
-        desc = str(args.get("description", "")).strip()
-        sa_name = str(args.get("subagent_type", "")).strip()
-        if not sa_name:
-            # Fallback to description snippet (may be empty during streaming)
-            sa_name = desc[:30] + "..." if len(desc) > 30 else desc
-        if not sa_name:
-            sa_name = "sub-agent"
-
-        if tool_id not in _announced_task_ids:
-            _announced_task_ids.append(tool_id)
-            _announced_names.append(sa_name)
-            _task_id_to_name[tool_id] = sa_name
-            return sa_name
-
-        # Update mapping if we learned a better name later
-        current = _task_id_to_name.get(tool_id, "sub-agent")
-        if sa_name != "sub-agent" and current != sa_name:
-            _task_id_to_name[tool_id] = sa_name
-            try:
-                idx = _announced_task_ids.index(tool_id)
-                if idx < len(_announced_names):
-                    _announced_names[idx] = sa_name
-            except ValueError:
-                pass
-            return sa_name
-        return None
-
-    def _extract_task_id(namespace: tuple) -> tuple[str | None, str | None]:
-        """Extract task tool_call_id from namespace if present.
-
-        Returns (task_id, task_ns_element) or (None, None).
-        """
-        for part in namespace:
-            part_str = str(part)
-            if "task:" in part_str:
-                tail = part_str.split("task:", 1)[1]
-                task_id = tail.split(":", 1)[0] if tail else ""
-                if task_id:
-                    return task_id, part_str
-        return None, None
-
-    def _next_announced_name() -> str | None:
-        """Get next announced name that hasn't been assigned yet."""
-        for announced in _announced_names:
-            if announced not in _assigned_names:
-                _assigned_names.add(announced)
-                return announced
-        return None
-
-    def _find_task_id_from_metadata(metadata: dict | None) -> str | None:
-        """Try to find a task tool_call_id in metadata."""
-        if not metadata:
-            return None
-        candidates = (
-            "tool_call_id",
-            "task_id",
-            "parent_run_id",
-            "root_run_id",
-            "run_id",
-        )
-        for key in candidates:
-            val = metadata.get(key)
-            if val and val in _task_id_to_name:
-                return val
-        return None
-
-    def _get_subagent_key(namespace: tuple, metadata: dict | None) -> str | None:
-        """Stable key for tracker/mapping per sub-agent namespace."""
-        if not namespace:
-            return None
-        task_id, task_ns = _extract_task_id(namespace)
-        if task_ns:
-            return task_ns
-        meta_task_id = _find_task_id_from_metadata(metadata)
-        if meta_task_id:
-            return f"task:{meta_task_id}"
-        if metadata:
-            for key in ("parent_run_id", "root_run_id", "run_id", "graph_id", "node_id"):
-                val = metadata.get(key)
-                if val:
-                    return f"{key}:{val}"
-        return str(namespace)
-
-    def _get_subagent_name(namespace: tuple, metadata: dict | None) -> str | None:
-        """Resolve sub-agent name from namespace, or None if main agent.
-
-        Priority:
-        0) metadata["lc_agent_name"] — most reliable, set by DeepAgents framework.
-        1) Match task_id embedded in namespace to announced tool_call_id.
-        2) Use cached key mapping (only real names, never "sub-agent").
-        3) Queue-based: assign next announced name to this key.
-        4) Fallback: return "sub-agent" WITHOUT caching.
-        """
-        if not namespace:
-            return None
-
-        key = _get_subagent_key(namespace, metadata) or str(namespace)
-
-        # 0) lc_agent_name from metadata — the REAL sub-agent name
-        #    set by the DeepAgents framework on every namespace event.
-        if metadata:
-            lc_name = metadata.get("lc_agent_name", "")
-            if isinstance(lc_name, str):
-                lc_name = lc_name.strip()
-            # Filter out generic/framework names
-            if lc_name and lc_name not in (
-                "sub-agent", "agent", "tools", "EvoScientist",
-                "LangGraph", "",
-            ):
-                _key_to_name[key] = lc_name
-                return lc_name
-
-        # 1) Resolve by task_id if present in namespace
-        task_id, _task_ns = _extract_task_id(namespace)
-        if task_id and task_id in _task_id_to_name:
-            name = _task_id_to_name[task_id]
-            if name and name != "sub-agent":
-                _assigned_names.add(name)
-                _key_to_name[key] = name
-                return name
-
-        meta_task_id = _find_task_id_from_metadata(metadata)
-        if meta_task_id and meta_task_id in _task_id_to_name:
-            name = _task_id_to_name[meta_task_id]
-            if name and name != "sub-agent":
-                _assigned_names.add(name)
-                _key_to_name[key] = name
-                return name
-
-        # 2) Cached real name for this key (skip if it's "sub-agent")
-        cached = _key_to_name.get(key)
-        if cached and cached != "sub-agent":
-            return cached
-
-        # 3) Assign next announced name from queue (skip "sub-agent" entries)
-        for announced in _announced_names:
-            if announced not in _assigned_names and announced != "sub-agent":
-                _assigned_names.add(announced)
-                _key_to_name[key] = announced
-                return announced
-
-        # 4) No real names available yet — return generic WITHOUT caching
-        return "sub-agent"
 
+def _shorten_path(path: str) -> str:
+    """Shorten absolute path to relative path from current directory."""
+    if not path:
+        return path
     try:
-        async for chunk in agent.astream(
-            {"messages": [{"role": "user", "content": message}]},
-            config=config,
-            stream_mode="messages",
-            subgraphs=True,
-        ):
-            # With subgraphs=True, event is (namespace, (message, metadata))
-            namespace: tuple = ()
-            data: Any = chunk
-
-            if isinstance(chunk, tuple) and len(chunk) >= 2:
-                first = chunk[0]
-                if isinstance(first, tuple):
-                    # (namespace_tuple, (message, metadata))
-                    namespace = first
-                    data = chunk[1]
-                else:
-                    # (message, metadata) — no namespace
-                    data = chunk
-
-            # Unpack message + metadata from data
-            msg: Any
-            metadata: dict = {}
-            if isinstance(data, tuple) and len(data) >= 2:
-                msg = data[0]
-                metadata = data[1] or {}
-            else:
-                msg = data
-
-            subagent = _get_subagent_name(namespace, metadata)
-            subagent_tracker = None
-            if subagent:
-                tracker_key = _get_subagent_key(namespace, metadata) or str(namespace)
-                subagent_tracker = _subagent_trackers.setdefault(tracker_key, ToolCallTracker())
-
-            # Process AIMessageChunk / AIMessage
-            if isinstance(msg, (AIMessageChunk, AIMessage)):
-                if subagent:
-                    # Sub-agent content — emit sub-agent events
-                    for ev in _process_chunk_content(msg, emitter, subagent_tracker):
-                        if ev.type == "tool_call":
-                            yield emitter.subagent_tool_call(
-                                subagent, ev.data["name"], ev.data["args"], ev.data.get("id", "")
-                            ).data
-                        # Skip text/thinking from sub-agents (too noisy)
-
-                    if hasattr(msg, "tool_calls") and msg.tool_calls:
-                        for tc in msg.tool_calls:
-                            name = tc.get("name", "")
-                            args = tc.get("args", {})
-                            tool_id = tc.get("id", "")
-                            # Skip empty-name chunks (incomplete streaming fragments)
-                            if not name and not tool_id:
-                                continue
-                            yield emitter.subagent_tool_call(
-                                subagent, name, args if isinstance(args, dict) else {}, tool_id
-                            ).data
-                else:
-                    # Main agent content
-                    for ev in _process_chunk_content(msg, emitter, main_tracker):
-                        if ev.type == "text":
-                            full_response += ev.data.get("content", "")
-                        yield ev.data
-
-                    if hasattr(msg, "tool_calls") and msg.tool_calls:
-                        for ev in _process_tool_calls(msg.tool_calls, emitter, main_tracker):
-                            yield ev.data
-                            # Detect task tool calls → announce sub-agent
-                            tc_data = ev.data
-                            if tc_data.get("name") == "task":
-                                started_name = _register_task_tool_call(tc_data)
-                                if started_name:
-                                    desc = str(tc_data.get("args", {}).get("description", "")).strip()
-                                    yield emitter.subagent_start(started_name, desc).data
-
-            # Process ToolMessage (tool execution result)
-            elif hasattr(msg, "type") and msg.type == "tool":
-                if subagent:
-                    if subagent_tracker:
-                        subagent_tracker.finalize_all()
-                        for info in subagent_tracker.emit_all_pending():
-                            yield emitter.subagent_tool_call(
-                                subagent,
-                                info.name,
-                                info.args,
-                                info.id,
-                            ).data
-                    name = getattr(msg, "name", "unknown")
-                    raw_content = str(getattr(msg, "content", ""))
-                    content = raw_content[:DisplayLimits.TOOL_RESULT_MAX]
-                    success = is_success(content)
-                    yield emitter.subagent_tool_result(subagent, name, content, success).data
-                else:
-                    for ev in _process_tool_result(msg, emitter, main_tracker):
-                        yield ev.data
-                        # Tool result can re-emit tool_call with full args; update task mapping
-                        if ev.type == "tool_call" and ev.data.get("name") == "task":
-                            started_name = _register_task_tool_call(ev.data)
-                            if started_name:
-                                desc = str(ev.data.get("args", {}).get("description", "")).strip()
-                                yield emitter.subagent_start(started_name, desc).data
-                    # Check if this is a task result → sub-agent ended
-                    name = getattr(msg, "name", "")
-                    if name == "task":
-                        tool_call_id = getattr(msg, "tool_call_id", "")
-                        # Find the sub-agent name via tool_call_id map
-                        sa_name = _task_id_to_name.get(tool_call_id, "sub-agent")
-                        yield emitter.subagent_end(sa_name).data
-
-    except Exception as e:
-        yield emitter.error(str(e)).data
-        raise
-
-    yield emitter.done(full_response).data
-
-
-def _process_chunk_content(chunk, emitter: StreamEventEmitter, tracker: ToolCallTracker):
-    """Process content blocks from an AI message chunk."""
-    content = chunk.content
-
-    if isinstance(content, str):
-        if content:
-            yield emitter.text(content)
-            return
-
-    blocks = None
-    if hasattr(chunk, "content_blocks"):
-        try:
-            blocks = chunk.content_blocks
-        except Exception:
-            blocks = None
-
-    if blocks is None:
-        if isinstance(content, dict):
-            blocks = [content]
-        elif isinstance(content, list):
-            blocks = content
-        else:
-            return
-
-    for raw_block in blocks:
-        block = raw_block
-        if not isinstance(block, dict):
-            if hasattr(block, "model_dump"):
-                block = block.model_dump()
-            elif hasattr(block, "dict"):
-                block = block.dict()
-            else:
-                continue
-
-        block_type = block.get("type")
-
-        if block_type in ("thinking", "reasoning"):
-            thinking_text = block.get("thinking") or block.get("reasoning") or ""
-            if thinking_text:
-                yield emitter.thinking(thinking_text)
-
-        elif block_type == "text":
-            text = block.get("text") or block.get("content") or ""
-            if text:
-                yield emitter.text(text)
-
-        elif block_type in ("tool_use", "tool_call"):
-            tool_id = block.get("id", "")
-            name = block.get("name", "")
-            args = block.get("input") if block_type == "tool_use" else block.get("args")
-            args_payload = args if isinstance(args, dict) else {}
-
-            if tool_id:
-                tracker.update(tool_id, name=name, args=args_payload)
-                if tracker.is_ready(tool_id):
-                    tracker.mark_emitted(tool_id)
-                    yield emitter.tool_call(name, args_payload, tool_id)
-
-        elif block_type == "input_json_delta":
-            partial_json = block.get("partial_json", "")
-            if partial_json:
-                tracker.append_json_delta(partial_json, block.get("index", 0))
-
-        elif block_type == "tool_call_chunk":
-            tool_id = block.get("id", "")
-            name = block.get("name", "")
-            if tool_id:
-                tracker.update(tool_id, name=name)
-            partial_args = block.get("args", "")
-            if isinstance(partial_args, str) and partial_args:
-                tracker.append_json_delta(partial_args, block.get("index", 0))
-
-
-def _process_tool_calls(tool_calls: list, emitter: StreamEventEmitter, tracker: ToolCallTracker):
-    """Process tool_calls from chunk.tool_calls attribute."""
-    for tc in tool_calls:
-        tool_id = tc.get("id", "")
-        if tool_id:
-            name = tc.get("name", "")
-            args = tc.get("args", {})
-            args_payload = args if isinstance(args, dict) else {}
-
-            tracker.update(tool_id, name=name, args=args_payload)
-            if tracker.is_ready(tool_id):
-                tracker.mark_emitted(tool_id)
-                yield emitter.tool_call(name, args_payload, tool_id)
-
-
-def _process_tool_result(chunk, emitter: StreamEventEmitter, tracker: ToolCallTracker):
-    """Process a ToolMessage result."""
-    tracker.finalize_all()
-
-    # Re-emit all tool calls with complete args
-    for info in tracker.get_all():
-        yield emitter.tool_call(info.name, info.args, info.id)
-
-    name = getattr(chunk, "name", "unknown")
-    raw_content = str(getattr(chunk, "content", ""))
-    content = raw_content[:DisplayLimits.TOOL_RESULT_MAX]
-    if len(raw_content) > DisplayLimits.TOOL_RESULT_MAX:
-        content += "\n... (truncated)"
-
-    success = is_success(content)
-    yield emitter.tool_result(name, content, success)
+        cwd = os.getcwd()
+        if path.startswith(cwd):
+            # Remove cwd prefix, keep the relative part
+            rel = path[len(cwd):].lstrip(os.sep)
+            # Add current dir name for context
+            return os.path.join(os.path.basename(cwd), rel) if rel else os.path.basename(cwd)
+        return path
+    except Exception:
+        return path
 
 
 # =============================================================================
-# Stream state
+# Banner
 # =============================================================================
 
-class SubAgentState:
-    """Tracks a single sub-agent's activity."""
+EVOSCIENTIST_ASCII_LINES = [
+    r" ███████╗ ██╗   ██╗  ██████╗  ███████╗  ██████╗ ██╗ ███████╗ ███╗   ██╗ ████████╗ ██╗ ███████╗ ████████╗",
+    r" ██╔════╝ ██║   ██║ ██╔═══██╗ ██╔════╝ ██╔════╝ ██║ ██╔════╝ ████╗  ██║ ╚══██╔══╝ ██║ ██╔════╝ ╚══██╔══╝",
+    r" █████╗   ██║   ██║ ██║   ██║ ███████╗ ██║      ██║ █████╗   ██╔██╗ ██║    ██║    ██║ ███████╗    ██║   ",
+    r" ██╔══╝   ╚██╗ ██╔╝ ██║   ██║ ╚════██║ ██║      ██║ ██╔══╝   ██║╚██╗██║    ██║    ██║ ╚════██║    ██║   ",
+    r" ███████╗  ╚████╔╝  ╚██████╔╝ ███████║ ╚██████╗ ██║ ███████╗ ██║ ╚████║    ██║    ██║ ███████║    ██║   ",
+    r" ╚══════╝   ╚═══╝    ╚═════╝  ╚══════╝  ╚═════╝ ╚═╝ ╚══════╝ ╚═╝  ╚═══╝    ╚═╝    ╚═╝ ╚══════╝    ╚═╝   ",
+]
 
-    def __init__(self, name: str, description: str = ""):
-        self.name = name
-        self.description = description
-        self.tool_calls: list[dict] = []
-        self.tool_results: list[dict] = []
-        self._result_map: dict[str, dict] = {}  # tool_call_id → result
-        self.is_active = True
+# Blue gradient: deep navy -> royal blue -> sky blue -> cyan
+_GRADIENT_COLORS = ["#1a237e", "#1565c0", "#1e88e5", "#42a5f5", "#64b5f6", "#90caf9"]
 
-    def add_tool_call(self, name: str, args: dict, tool_id: str = ""):
-        # Skip empty-name calls without an id (incomplete streaming chunks)
-        if not name and not tool_id:
-            return
-        tc_data = {"id": tool_id, "name": name, "args": args}
-        if tool_id:
-            for i, tc in enumerate(self.tool_calls):
-                if tc.get("id") == tool_id:
-                    # Merge: keep the non-empty name/args
-                    if name:
-                        self.tool_calls[i]["name"] = name
-                    if args:
-                        self.tool_calls[i]["args"] = args
-                    return
-        # Skip if name is empty and we can't deduplicate by id
-        if not name:
-            return
-        self.tool_calls.append(tc_data)
-
-    def add_tool_result(self, name: str, content: str, success: bool = True):
-        result = {"name": name, "content": content, "success": success}
-        self.tool_results.append(result)
-        # Try to match result to the first unmatched tool call with same name
-        for tc in self.tool_calls:
-            tc_id = tc.get("id", "")
-            tc_name = tc.get("name", "")
-            if tc_id and tc_id not in self._result_map and tc_name == name:
-                self._result_map[tc_id] = result
-                return
-        # Fallback: match first unmatched tool call
-        for tc in self.tool_calls:
-            tc_id = tc.get("id", "")
-            if tc_id and tc_id not in self._result_map:
-                self._result_map[tc_id] = result
-                return
-
-    def get_result_for(self, tc: dict) -> dict | None:
-        """Get matched result for a tool call."""
-        tc_id = tc.get("id", "")
-        if tc_id:
-            return self._result_map.get(tc_id)
-        # Fallback: index-based matching
-        try:
-            idx = self.tool_calls.index(tc)
-            if idx < len(self.tool_results):
-                return self.tool_results[idx]
-        except ValueError:
-            pass
-        return None
-
-
-class StreamState:
-    """Accumulates stream state for display updates."""
-
-    def __init__(self):
-        self.thinking_text = ""
-        self.response_text = ""
-        self.tool_calls = []
-        self.tool_results = []
-        self.is_thinking = False
-        self.is_responding = False
-        self.is_processing = False
-        # Sub-agent tracking
-        self.subagents: list[SubAgentState] = []
-        self._subagent_map: dict[str, SubAgentState] = {}  # name → state
-        # Todo list tracking
-        self.todo_items: list[dict] = []
-        # Latest text segment (reset on each tool_call)
-        self.latest_text = ""
-
-    def _get_or_create_subagent(self, name: str, description: str = "") -> SubAgentState:
-        if name not in self._subagent_map:
-            # Case 1: real name arrives, "sub-agent" entry exists → rename it
-            if name != "sub-agent" and "sub-agent" in self._subagent_map:
-                old_sa = self._subagent_map.pop("sub-agent")
-                old_sa.name = name
-                if description:
-                    old_sa.description = description
-                self._subagent_map[name] = old_sa
-                return old_sa
-            # Case 2: "sub-agent" arrives but a pre-registered real-name entry
-            #         exists with no tool calls → merge into it
-            if name == "sub-agent":
-                active_named = [
-                    sa for sa in self.subagents
-                    if sa.is_active and sa.name != "sub-agent"
-                ]
-                if len(active_named) == 1 and not active_named[0].tool_calls:
-                    self._subagent_map[name] = active_named[0]
-                    return active_named[0]
-            sa = SubAgentState(name, description)
-            self.subagents.append(sa)
-            self._subagent_map[name] = sa
-        else:
-            existing = self._subagent_map[name]
-            if description and not existing.description:
-                existing.description = description
-            # If this entry was created as "sub-agent" placeholder and the
-            # actual name is different, update.
-            if name != "sub-agent" and existing.name == "sub-agent":
-                existing.name = name
-        return self._subagent_map[name]
-
-    def _resolve_subagent_name(self, name: str) -> str:
-        """Resolve "sub-agent" to the single active named sub-agent when possible."""
-        if name != "sub-agent":
-            return name
-        active_named = [
-            sa.name for sa in self.subagents
-            if sa.is_active and sa.name != "sub-agent"
-        ]
-        if len(active_named) == 1:
-            return active_named[0]
-        return name
-
-    def handle_event(self, event: dict) -> str:
-        """Process a single stream event, update internal state, return event type."""
-        event_type: str = event.get("type", "")
-
-        if event_type == "thinking":
-            self.is_thinking = True
-            self.is_responding = False
-            self.is_processing = False
-            self.thinking_text += event.get("content", "")
-
-        elif event_type == "text":
-            self.is_thinking = False
-            self.is_responding = True
-            self.is_processing = False
-            text_content = event.get("content", "")
-            self.response_text += text_content
-            self.latest_text += text_content
-
-        elif event_type == "tool_call":
-            self.is_thinking = False
-            self.is_responding = False
-            self.is_processing = False
-            self.latest_text = ""  # Reset — next text segment is a new message
-
-            tool_id = event.get("id", "")
-            tool_name = event.get("name", "unknown")
-            tool_args = event.get("args", {})
-            tc_data = {
-                "id": tool_id,
-                "name": tool_name,
-                "args": tool_args,
-            }
-
-            if tool_id:
-                updated = False
-                for i, tc in enumerate(self.tool_calls):
-                    if tc.get("id") == tool_id:
-                        self.tool_calls[i] = tc_data
-                        updated = True
-                        break
-                if not updated:
-                    self.tool_calls.append(tc_data)
-            else:
-                self.tool_calls.append(tc_data)
-
-            # Capture todo items from write_todos args (most reliable source)
-            if tool_name == "write_todos":
-                todos = tool_args.get("todos", [])
-                if isinstance(todos, list) and todos:
-                    self.todo_items = todos
-
-        elif event_type == "tool_result":
-            self.is_processing = True
-            result_name = event.get("name", "unknown")
-            result_content = event.get("content", "")
-            self.tool_results.append({
-                "name": result_name,
-                "content": result_content,
-            })
-            # Update todo list from write_todos / read_todos results (fallback)
-            if result_name in ("write_todos", "read_todos"):
-                parsed = _parse_todo_items(result_content)
-                if parsed:
-                    self.todo_items = parsed
-
-        elif event_type == "subagent_start":
-            name = event.get("name", "sub-agent")
-            desc = event.get("description", "")
-            sa = self._get_or_create_subagent(name, desc)
-            sa.is_active = True
-
-        elif event_type == "subagent_tool_call":
-            sa_name = self._resolve_subagent_name(event.get("subagent", "sub-agent"))
-            sa = self._get_or_create_subagent(sa_name)
-            sa.add_tool_call(
-                event.get("name", "unknown"),
-                event.get("args", {}),
-                event.get("id", ""),
-            )
-
-        elif event_type == "subagent_tool_result":
-            sa_name = self._resolve_subagent_name(event.get("subagent", "sub-agent"))
-            sa = self._get_or_create_subagent(sa_name)
-            sa.add_tool_result(
-                event.get("name", "unknown"),
-                event.get("content", ""),
-                event.get("success", True),
-            )
-
-        elif event_type == "subagent_end":
-            name = self._resolve_subagent_name(event.get("name", "sub-agent"))
-            if name in self._subagent_map:
-                self._subagent_map[name].is_active = False
-            elif name == "sub-agent":
-                # Couldn't resolve — deactivate the oldest active sub-agent
-                for sa in self.subagents:
-                    if sa.is_active:
-                        sa.is_active = False
-                        break
-
-        elif event_type == "done":
-            self.is_processing = False
-            if not self.response_text:
-                self.response_text = event.get("response", "")
-
-        elif event_type == "error":
-            self.is_processing = False
-            self.is_thinking = False
-            self.is_responding = False
-            error_msg = event.get("message", "Unknown error")
-            self.response_text += f"\n\n[Error] {error_msg}"
-
-        return event_type
-
-    def get_display_args(self) -> dict:
-        """Get kwargs for create_streaming_display()."""
-        return {
-            "thinking_text": self.thinking_text,
-            "response_text": self.response_text,
-            "latest_text": self.latest_text,
-            "tool_calls": self.tool_calls,
-            "tool_results": self.tool_results,
-            "is_thinking": self.is_thinking,
-            "is_responding": self.is_responding,
-            "is_processing": self.is_processing,
-            "subagents": self.subagents,
-            "todo_items": self.todo_items,
-        }
+
+def print_banner(
+    thread_id: str,
+    workspace_dir: str | None = None,
+    memory_dir: str | None = None,
+    mode: str | None = None,
+    model: str | None = None,
+    provider: str | None = None,
+):
+    """Print welcome banner with ASCII art logo, thread ID, workspace path, and mode."""
+    for line, color in zip(EVOSCIENTIST_ASCII_LINES, _GRADIENT_COLORS):
+        console.print(Text(line, style=f"{color} bold"))
+    info = Text()
+    info.append("  Thread: ", style="dim")
+    info.append(thread_id, style="yellow")
+    if workspace_dir:
+        info.append("\n  Workspace: ", style="dim")
+        info.append(_shorten_path(workspace_dir), style="cyan")
+    if memory_dir:
+        trimmed = memory_dir.rstrip("/").rstrip("\\")
+        info.append("\n  Memory dir: ", style="dim")
+        info.append(_shorten_path(trimmed), style="cyan")
+    if model or provider or mode:
+        info.append("\n  ", style="dim")
+        parts = []
+        if model:
+            parts.append(("Model: ", model))
+        if provider:
+            parts.append(("Provider: ", provider))
+        if mode:
+            parts.append(("Mode: ", mode))
+        for i, (label, value) in enumerate(parts):
+            if i > 0:
+                info.append("  ", style="dim")
+            info.append(label, style="dim")
+            info.append(value, style="magenta")
+    info.append("\n  Commands: ", style="dim")
+    info.append("/exit", style="bold")
+    info.append(", ", style="dim")
+    info.append("/new", style="bold")
+    info.append(", ", style="dim")
+    info.append("/thread", style="bold")
+    info.append(", ", style="dim")
+    info.append("/skills", style="bold")
+    info.append(", ", style="dim")
+    info.append("/install-skill", style="bold")
+    info.append(", ", style="dim")
+    info.append("/uninstall-skill", style="bold")
+    console.print(info)
+    console.print()
 
 
 # =============================================================================
-# Display functions
+# Skill management commands
 # =============================================================================
 
-def _parse_todo_items(content: str) -> list[dict] | None:
-    """Parse todo items from write_todos output.
 
-    Attempts to extract a list of dicts with 'status' and 'content' keys
-    from the tool result string. Returns None if parsing fails.
-
-    Handles formats like:
-      - Raw JSON/Python list: [{"content": "...", "status": "..."}]
-      - Prefixed: "Updated todo list to [{'content': '...', ...}]"
-    """
-    import ast
-    import json
-
-    content = content.strip()
-
-    def _try_parse(text: str) -> list[dict] | None:
-        """Try JSON then Python literal parsing."""
-        text = text.strip()
-        try:
-            data = json.loads(text)
-            if isinstance(data, list) and data and isinstance(data[0], dict):
-                return data
-        except (json.JSONDecodeError, ValueError):
-            pass
-        try:
-            data = ast.literal_eval(text)
-            if isinstance(data, list) and data and isinstance(data[0], dict):
-                return data
-        except (ValueError, SyntaxError):
-            pass
-        return None
-
-    # Try the full content directly
-    result = _try_parse(content)
-    if result:
-        return result
-
-    # Extract embedded [...] from content (e.g. "Updated todo list to [{...}]")
-    bracket_start = content.find("[")
-    if bracket_start != -1:
-        bracket_end = content.rfind("]")
-        if bracket_end > bracket_start:
-            embedded = content[bracket_start:bracket_end + 1]
-            result = _try_parse(embedded)
-            if result:
-                return result
-
-    # Try line-by-line scan
-    for line in content.split("\n"):
-        line = line.strip()
-        if "[" in line:
-            start = line.find("[")
-            end = line.rfind("]")
-            if end > start:
-                result = _try_parse(line[start:end + 1])
-                if result:
-                    return result
-
-    return None
-
-
-def _build_todo_stats(items: list[dict]) -> str:
-    """Build stats string like '2 active | 1 pending | 3 done'."""
-    counts: dict[str, int] = {}
-    for item in items:
-        status = str(item.get("status", "todo")).lower()
-        # Normalize status names
-        if status in ("done", "completed", "complete"):
-            status = "done"
-        elif status in ("active", "in_progress", "in-progress", "working"):
-            status = "active"
-        else:
-            status = "pending"
-        counts[status] = counts.get(status, 0) + 1
-
-    parts = []
-    for key in ("active", "pending", "done"):
-        if counts.get(key, 0) > 0:
-            parts.append(f"{counts[key]} {key}")
-    return " | ".join(parts) if parts else f"{len(items)} items"
-
-
-def _format_single_todo(item: dict) -> Text:
-    """Format a single todo item with status symbol."""
-    status = str(item.get("status", "todo")).lower()
-    content_text = str(item.get("content", item.get("task", item.get("title", ""))))
-
-    if status in ("done", "completed", "complete"):
-        symbol = "\u2713"
-        label = "done  "
-        style = "green dim"
-    elif status in ("active", "in_progress", "in-progress", "working"):
-        symbol = "\u25cf"
-        label = "active"
-        style = "yellow"
-    else:
-        symbol = "\u25cb"
-        label = "todo  "
-        style = "dim"
+def _cmd_list_skills() -> None:
+    """List installed user skills."""
+    from .skills_manager import list_skills
+    from .paths import USER_SKILLS_DIR
 
-    line = Text()
-    line.append(f"    {symbol} ", style=style)
-    line.append(label, style=style)
-    line.append(" ", style="dim")
-    # Truncate long content
-    if len(content_text) > 60:
-        content_text = content_text[:57] + "..."
-    line.append(content_text, style=style)
-    return line
+    skills = list_skills(include_system=False)
 
+    if not skills:
+        console.print("[dim]No user skills installed.[/dim]")
+        console.print("[dim]Install with:[/dim] /install-skill <path-or-url>")
+        console.print(f"[dim]Skills directory:[/dim] [cyan]{_shorten_path(str(USER_SKILLS_DIR))}[/cyan]")
+        console.print()
+        return
 
-def format_tool_result_compact(_name: str, content: str, max_lines: int = 5) -> list:
-    """Format tool result as tree output.
+    console.print(f"[bold]Installed Skills[/bold] ({len(skills)}):")
+    for skill in skills:
+        console.print(f"  [green]{skill.name}[/green] - {skill.description}")
+    console.print(f"\n[dim]Location:[/dim] [cyan]{_shorten_path(str(USER_SKILLS_DIR))}[/cyan]")
+    console.print()
 
-    Special handling for write_todos: shows formatted checklist with status symbols.
-    """
-    elements = []
-
-    if not content.strip():
-        elements.append(Text("  \u2514 (empty)", style="dim"))
-        return elements
-
-    # Special handling for write_todos
-    if _name == "write_todos":
-        items = _parse_todo_items(content)
-        if items:
-            stats = _build_todo_stats(items)
-            stats_line = Text()
-            stats_line.append("  \u2514 ", style="dim")
-            stats_line.append(stats, style="dim")
-            elements.append(stats_line)
-            elements.append(Text("", style="dim"))  # blank line
-
-            max_preview = 4
-            for item in items[:max_preview]:
-                elements.append(_format_single_todo(item))
-
-            remaining = len(items) - max_preview
-            if remaining > 0:
-                elements.append(Text(f"    ... {remaining} more", style="dim italic"))
-
-            return elements
-
-    lines = content.strip().split("\n")
-    total_lines = len(lines)
-
-    display_lines = lines[:max_lines]
-    for i, line in enumerate(display_lines):
-        prefix = "\u2514" if i == 0 else " "
-        if len(line) > 80:
-            line = line[:77] + "..."
-        style = "dim" if is_success(content) else "red dim"
-        elements.append(Text(f"  {prefix} {line}", style=style))
-
-    remaining = total_lines - max_lines
-    if remaining > 0:
-        elements.append(Text(f"    ... +{remaining} lines", style="dim italic"))
-
-    return elements
-
-
-def _render_tool_call_line(tc: dict, tr: dict | None) -> Text:
-    """Render a single tool call line with status indicator."""
-    is_task = tc.get('name', '').lower() == 'task'
-
-    if tr is not None:
-        content = tr.get('content', '')
-        if is_success(content):
-            style = "bold green"
-            indicator = "\u2713" if is_task else ToolStatus.SUCCESS.value
-        else:
-            style = "bold red"
-            indicator = "\u2717" if is_task else ToolStatus.ERROR.value
-    else:
-        style = "bold yellow" if not is_task else "bold cyan"
-        indicator = "\u25b6" if is_task else ToolStatus.RUNNING.value
 
-    tool_compact = format_tool_compact(tc['name'], tc.get('args'))
-    tool_text = Text()
-    tool_text.append(f"{indicator} ", style=style)
-    tool_text.append(tool_compact, style=style)
-    return tool_text
+def _cmd_install_skill(source: str) -> None:
+    """Install a skill from local path or GitHub URL."""
+    from .skills_manager import install_skill
 
+    if not source:
+        console.print("[red]Usage:[/red] /install-skill <path-or-url>")
+        console.print("[dim]Examples:[/dim]")
+        console.print("  /install-skill ./my-skill")
+        console.print("  /install-skill https://github.com/user/repo/tree/main/skill-name")
+        console.print("  /install-skill user/repo@skill-name")
+        console.print()
+        return
 
-def _render_subagent_section(sa: 'SubAgentState', compact: bool = False) -> list:
-    """Render a sub-agent's activity as a bordered section.
+    console.print(f"[dim]Installing skill from:[/dim] {source}")
 
-    Args:
-        sa: Sub-agent state to render
-        compact: If True, render minimal 1-line summary (completed sub-agents)
+    result = install_skill(source)
 
-    Header uses "Cooking with {name}" style matching task tool format.
-    Active sub-agents show bordered tool list; completed ones collapse to 1 line.
-    """
-    elements = []
-    BORDER = "dim cyan" if sa.is_active else "dim"
-
-    # Filter out tool calls with empty names
-    valid_calls = [tc for tc in sa.tool_calls if tc.get("name")]
-
-    # Split into completed and pending
-    completed = []
-    pending = []
-    for tc in valid_calls:
-        tr = sa.get_result_for(tc)
-        if tr is not None:
-            completed.append((tc, tr))
-        else:
-            pending.append(tc)
-
-    succeeded = sum(1 for _, tr in completed if tr.get("success", True))
-    failed = len(completed) - succeeded
-
-    # Build display name
-    display_name = f"Cooking with {sa.name}"
-    if sa.description:
-        desc = sa.description[:50] + "..." if len(sa.description) > 50 else sa.description
-        display_name += f" \u2014 {desc}"
-
-    # --- Compact mode: 1-line summary for completed sub-agents ---
-    if compact:
-        line = Text()
-        if not sa.is_active:
-            line.append("\u2713 ", style="green")
-            line.append(display_name, style="green dim")
-            total = len(valid_calls)
-            line.append(f" ({total} tools)", style="dim")
-        else:
-            line.append("\u25b6 ", style="cyan")
-            line.append(display_name, style="bold cyan")
-        elements.append(line)
-        return elements
-
-    # --- Full mode: bordered section for Live streaming ---
-
-    # Header
-    header = Text()
-    header.append("\u250c ", style=BORDER)
-    if sa.is_active:
-        header.append(f"\u25b6 {display_name}", style="bold cyan")
+    if result["success"]:
+        console.print(f"[green]Installed:[/green] {result['name']}")
+        console.print(f"[dim]Description:[/dim] {result.get('description', '(none)')}")
+        console.print(f"[dim]Path:[/dim] [cyan]{_shorten_path(result['path'])}[/cyan]")
+        console.print()
+        console.print("[dim]Reload the agent with /new to use the skill.[/dim]")
     else:
-        header.append(f"\u2713 {display_name}", style="bold green")
-    elements.append(header)
-
-    # Show every tool call with its status
-    for tc, tr in completed:
-        tc_line = Text("\u2502 ", style=BORDER)
-        tc_name = format_tool_compact(tc["name"], tc.get("args"))
-        if tr.get("success", True):
-            tc_line.append(f"\u2713 {tc_name}", style="green")
-        else:
-            tc_line.append(f"\u2717 {tc_name}", style="red")
-            content = tr.get("content", "")
-            first_line = content.strip().split("\n")[0][:70]
-            if first_line:
-                err_line = Text("\u2502   ", style=BORDER)
-                err_line.append(f"\u2514 {first_line}", style="red dim")
-                elements.append(tc_line)
-                elements.append(err_line)
-                continue
-        elements.append(tc_line)
-
-    # Pending/running tools
-    for tc in pending:
-        tc_line = Text("\u2502 ", style=BORDER)
-        tc_name = format_tool_compact(tc["name"], tc.get("args"))
-        tc_line.append(f"\u25cf {tc_name}", style="bold yellow")
-        elements.append(tc_line)
-        spinner_line = Text("\u2502   ", style=BORDER)
-        spinner_line.append("\u21bb running...", style="yellow dim")
-        elements.append(spinner_line)
-
-    # Footer
-    if not sa.is_active:
-        total = len(valid_calls)
-        footer = Text(f"\u2514 done ({total} tools)", style="dim green")
-        elements.append(footer)
-    elif valid_calls:
-        footer = Text("\u2514 running...", style="dim cyan")
-        elements.append(footer)
-
-    return elements
-
-
-def _render_todo_panel(todo_items: list[dict]) -> Panel:
-    """Render a bordered Task List panel from todo items.
-
-    Matches the style: cyan border, status icons per item.
-    """
-    lines = Text()
-    for i, item in enumerate(todo_items):
-        if i > 0:
-            lines.append("\n")
-        status = str(item.get("status", "todo")).lower()
-        content_text = str(item.get("content", item.get("task", item.get("title", ""))))
-
-        if status in ("done", "completed", "complete"):
-            symbol = "\u2713"  # ✓
-            style = "green dim"
-        elif status in ("active", "in_progress", "in-progress", "working"):
-            symbol = "\u23f3"  # ⏳
-            style = "yellow"
-        else:
-            symbol = "\u25a1"  # □
-            style = "dim"
-
-        lines.append(f"{symbol} ", style=style)
-        lines.append(content_text, style=style)
-
-    return Panel(
-        lines,
-        title="Task List",
-        title_align="center",
-        border_style="cyan",
-        padding=(0, 1),
-    )
-
-
-def create_streaming_display(
-    thinking_text: str = "",
-    response_text: str = "",
-    latest_text: str = "",
-    tool_calls: list | None = None,
-    tool_results: list | None = None,
-    is_thinking: bool = False,
-    is_responding: bool = False,
-    is_waiting: bool = False,
-    is_processing: bool = False,
-    show_thinking: bool = True,
-    subagents: list | None = None,
-    todo_items: list | None = None,
-) -> Any:
-    """Create Rich display layout for streaming output.
+        console.print(f"[red]Failed:[/red] {result['error']}")
+    console.print()
 
-    Returns:
-        Rich Group for Live display
-    """
-    elements = []
-    tool_calls = tool_calls or []
-    tool_results = tool_results or []
-    subagents = subagents or []
-
-    # Initial waiting state
-    if is_waiting and not thinking_text and not response_text and not tool_calls:
-        spinner = Spinner("dots", text=" Thinking...", style="cyan")
-        elements.append(spinner)
-        return Group(*elements)
-
-    # Thinking panel
-    if show_thinking and thinking_text:
-        thinking_title = "Thinking"
-        if is_thinking:
-            thinking_title += " ..."
-        display_thinking = thinking_text
-        if len(display_thinking) > DisplayLimits.THINKING_STREAM:
-            display_thinking = "..." + display_thinking[-DisplayLimits.THINKING_STREAM:]
-        elements.append(Panel(
-            Text(display_thinking, style="dim"),
-            title=thinking_title,
-            border_style="blue",
-            padding=(0, 1),
-        ))
-
-    # Tool calls and results paired display
-    # Collapse older completed tools to prevent overflow in Live mode
-    # Task tool calls are ALWAYS visible (they represent sub-agent delegations)
-    MAX_VISIBLE_TOOLS = 4
-    MAX_VISIBLE_RUNNING = 3
-
-    if tool_calls:
-        # Split into categories
-        completed_regular = []   # completed non-task tools
-        task_tools = []          # task tools (always visible)
-        running_regular = []     # running non-task tools
-
-        for i, tc in enumerate(tool_calls):
-            has_result = i < len(tool_results)
-            tr = tool_results[i] if has_result else None
-            is_task = tc.get('name') == 'task'
-
-            if is_task:
-                # Skip task calls with empty args (still streaming)
-                if tc.get('args'):
-                    task_tools.append((tc, tr))
-            elif has_result:
-                completed_regular.append((tc, tr))
-            else:
-                running_regular.append((tc, None))
-
-        # --- Completed regular tools (collapsible) ---
-        slots = max(0, MAX_VISIBLE_TOOLS - len(running_regular))
-        hidden = completed_regular[:-slots] if slots and len(completed_regular) > slots else (completed_regular if not slots else [])
-        visible = completed_regular[-slots:] if slots else []
-
-        if hidden:
-            ok = sum(1 for _, tr in hidden if is_success(tr.get('content', '')))
-            fail = len(hidden) - ok
-            summary = Text()
-            summary.append(f"\u2713 {ok} completed", style="dim green")
-            if fail > 0:
-                summary.append(f" | {fail} failed", style="dim red")
-            elements.append(summary)
-
-        for tc, tr in visible:
-            elements.append(_render_tool_call_line(tc, tr))
-            content = tr.get('content', '') if tr else ''
-            if tr and not is_success(content):
-                result_elements = format_tool_result_compact(
-                    tr['name'], content, max_lines=5,
-                )
-                elements.extend(result_elements)
-
-        # --- Running regular tools (limit visible) ---
-        hidden_running = len(running_regular) - MAX_VISIBLE_RUNNING
-        if hidden_running > 0:
-            summary = Text()
-            summary.append(f"\u25cf {hidden_running} more running...", style="dim yellow")
-            elements.append(summary)
-            running_regular = running_regular[-MAX_VISIBLE_RUNNING:]
-
-        for tc, tr in running_regular:
-            elements.append(_render_tool_call_line(tc, tr))
-            spinner = Spinner("dots", text=" Running...", style="yellow")
-            elements.append(spinner)
-
-        # Task tool calls are rendered as part of sub-agent sections below
-
-    # Response text handling
-    has_pending_tools = len(tool_calls) > len(tool_results)
-    any_active_subagent = any(sa.is_active for sa in subagents)
-    has_used_tools = len(tool_calls) > 0
-    all_done = not has_pending_tools and not any_active_subagent and not is_processing
-
-    # Intermediate narration (tools still running) — dim italic above Task List
-    if latest_text and has_used_tools and not all_done:
-        preview = latest_text.strip()
-        if preview:
-            last_line = preview.split("\n")[-1].strip()
-            if last_line:
-                if len(last_line) > 80:
-                    last_line = last_line[:77] + "..."
-                elements.append(Text(f"    {last_line}", style="dim italic"))
-
-    # Task List panel (persistent, updates on write_todos / read_todos)
-    todo_items = todo_items or []
-    if todo_items:
-        elements.append(Text(""))  # blank separator
-        elements.append(_render_todo_panel(todo_items))
-
-    # Sub-agent activity sections
-    # Active: full bordered view; Completed: compact 1-line summary
-    for sa in subagents:
-        if sa.tool_calls or sa.is_active:
-            elements.extend(_render_subagent_section(sa, compact=not sa.is_active))
-
-    # Processing state after tool execution
-    if is_processing and not is_thinking and not is_responding and not response_text:
-        # Check if any sub-agent is active
-        any_active = any(sa.is_active for sa in subagents)
-        if not any_active:
-            spinner = Spinner("dots", text=" Analyzing results...", style="cyan")
-            elements.append(spinner)
-
-    # Final response — render as Markdown when all work is done
-    if response_text and all_done:
-        elements.append(Text(""))  # blank separator
-        elements.append(Markdown(response_text))
-    elif is_responding and not thinking_text and not has_pending_tools:
-        elements.append(Text("Generating response...", style="dim"))
-
-    return Group(*elements) if elements else Text("Processing...", style="dim")
-
-
-def display_final_results(
-    state: StreamState,
-    thinking_max_length: int = DisplayLimits.THINKING_FINAL,
-    show_thinking: bool = True,
-    show_tools: bool = True,
-) -> None:
-    """Display final results after streaming completes."""
-    if show_thinking and state.thinking_text:
-        display_thinking = state.thinking_text
-        if len(display_thinking) > thinking_max_length:
-            half = thinking_max_length // 2
-            display_thinking = display_thinking[:half] + "\n\n... (truncated) ...\n\n" + display_thinking[-half:]
-        console.print(Panel(
-            Text(display_thinking, style="dim"),
-            title="Thinking",
-            border_style="blue",
-        ))
-
-    if show_tools and state.tool_calls:
-        shown_sa_names: set[str] = set()
-
-        for i, tc in enumerate(state.tool_calls):
-            has_result = i < len(state.tool_results)
-            tr = state.tool_results[i] if has_result else None
-            content = tr.get('content', '') if tr is not None else ''
-            is_task = tc.get('name', '').lower() == 'task'
-
-            # Task tools: show delegation line + compact sub-agent summary
-            if is_task:
-                console.print(_render_tool_call_line(tc, tr))
-                sa_name = tc.get('args', {}).get('subagent_type', '')
-                task_desc = tc.get('args', {}).get('description', '')
-                matched_sa = None
-                for sa in state.subagents:
-                    if sa.name == sa_name or (task_desc and task_desc in (sa.description or '')):
-                        matched_sa = sa
-                        break
-                if matched_sa:
-                    shown_sa_names.add(matched_sa.name)
-                    for elem in _render_subagent_section(matched_sa, compact=True):
-                        console.print(elem)
-                continue
 
-            # Regular tools: show tool call line + result
-            console.print(_render_tool_call_line(tc, tr))
-            if has_result and tr is not None:
-                result_elements = format_tool_result_compact(
-                    tr['name'],
-                    content,
-                    max_lines=10,
-                )
-                for elem in result_elements:
-                    console.print(elem)
-
-        # Render any sub-agents not already shown via task tool calls
-        for sa in state.subagents:
-            if sa.name not in shown_sa_names and (sa.tool_calls or sa.is_active):
-                for elem in _render_subagent_section(sa, compact=True):
-                    console.print(elem)
+def _cmd_uninstall_skill(name: str) -> None:
+    """Uninstall a user-installed skill."""
+    from .skills_manager import uninstall_skill
 
+    if not name:
+        console.print("[red]Usage:[/red] /uninstall-skill <skill-name>")
+        console.print("[dim]Use /skills to see installed skills.[/dim]")
         console.print()
+        return
 
-    # Task List panel in final output
-    if state.todo_items:
-        console.print(_render_todo_panel(state.todo_items))
-        console.print()
+    result = uninstall_skill(name)
 
-    if state.response_text:
-        console.print()
-        console.print(Markdown(state.response_text))
-        console.print()
-
-
-# =============================================================================
-# Async-to-sync bridge
-# =============================================================================
-
-def _run_streaming(
-    agent: Any,
-    message: str,
-    thread_id: str,
-    show_thinking: bool,
-    interactive: bool,
-) -> None:
-    """Run async streaming and render with Rich Live display.
-
-    Bridges the async stream_agent_events() into synchronous Rich Live rendering
-    using asyncio.run().
-
-    Args:
-        agent: Compiled agent graph
-        message: User message
-        thread_id: Thread ID
-        show_thinking: Whether to show thinking panel
-        interactive: If True, use simplified final display (no panel)
-    """
-    state = StreamState()
-
-    async def _consume() -> None:
-        async for event in stream_agent_events(agent, message, thread_id):
-            event_type = state.handle_event(event)
-            live.update(create_streaming_display(
-                **state.get_display_args(),
-                show_thinking=show_thinking,
-            ))
-            if event_type in (
-                "tool_call", "tool_result",
-                "subagent_start", "subagent_tool_call",
-                "subagent_tool_result", "subagent_end",
-            ):
-                live.refresh()
-
-    with Live(console=console, refresh_per_second=10, transient=True) as live:
-        live.update(create_streaming_display(is_waiting=True))
-        asyncio.run(_consume())
-
-    if interactive:
-        display_final_results(
-            state,
-            thinking_max_length=500,
-            show_thinking=False,
-            show_tools=True,
-        )
+    if result["success"]:
+        console.print(f"[green]Uninstalled:[/green] {name}")
+        console.print("[dim]Reload the agent with /new to apply changes.[/dim]")
     else:
-        console.print()
-        display_final_results(
-            state,
-            show_tools=True,
-        )
+        console.print(f"[red]Failed:[/red] {result['error']}")
+    console.print()
 
 
 # =============================================================================
 # CLI commands
 # =============================================================================
 
-EVOSCIENTIST_ASCII_LINES = [
-    r" ███████╗ ██╗   ██╗  ██████╗  ███████╗  ██████╗ ██╗ ███████╗ ███╗   ██╗ ████████╗ ██╗ ███████╗ ████████╗",
-    r" ██╔════╝ ██║   ██║ ██╔═══██╗ ██╔════╝ ██╔════╝ ██║ ██╔════╝ ████╗  ██║ ╚══██╔══╝ ██║ ██╔════╝ ╚══██╔══╝",
-    r" █████╗   ██║   ██║ ██║   ██║ ███████╗ ██║      ██║ █████╗   ██╔██╗ ██║    ██║    ██║ ███████╗    ██║   ",
-    r" ██╔══╝   ╚██╗ ██╔╝ ██║   ██║ ╚════██║ ██║      ██║ ██╔══╝   ██║╚██╗██║    ██║    ██║ ╚════██║    ██║   ",
-    r" ███████╗  ╚████╔╝  ╚██████╔╝ ███████║ ╚██████╗ ██║ ███████╗ ██║ ╚████║    ██║    ██║ ███████║    ██║   ",
-    r" ╚══════╝   ╚═══╝    ╚═════╝  ╚══════╝  ╚═════╝ ╚═╝ ╚══════╝ ╚═╝  ╚═══╝    ╚═╝    ╚═╝ ╚══════╝    ╚═╝   ",
-]
-
-# Blue gradient: deep navy → royal blue → sky blue → cyan
-_GRADIENT_COLORS = ["#1a237e", "#1565c0", "#1e88e5", "#42a5f5", "#64b5f6", "#90caf9"]
-
-
-def print_banner(thread_id: str, workspace_dir: str | None = None):
-    """Print welcome banner with ASCII art logo, thread ID, and workspace path."""
-    for line, color in zip(EVOSCIENTIST_ASCII_LINES, _GRADIENT_COLORS):
-        console.print(Text(line, style=f"{color} bold"))
-    info = Text()
-    info.append("  Thread: ", style="dim")
-    info.append(thread_id, style="yellow")
-    if workspace_dir:
-        info.append("\n  Workspace: ", style="dim")
-        info.append(workspace_dir, style="cyan")
-    info.append("\n  Commands: ", style="dim")
-    info.append("/exit", style="bold")
-    info.append(", ", style="dim")
-    info.append("/new", style="bold")
-    info.append(" (new session), ", style="dim")
-    info.append("/thread", style="bold")
-    info.append(" (show thread ID)", style="dim")
-    console.print(info)
-    console.print()
-
-
-def cmd_interactive(agent: Any, show_thinking: bool = True, workspace_dir: str | None = None) -> None:
+def cmd_interactive(
+    agent: Any,
+    show_thinking: bool = True,
+    workspace_dir: str | None = None,
+    workspace_fixed: bool = False,
+    mode: str | None = None,
+    model: str | None = None,
+    provider: str | None = None,
+) -> None:
     """Interactive conversation mode with streaming output.
 
     Args:
         agent: Compiled agent graph
         show_thinking: Whether to display thinking panels
         workspace_dir: Per-session workspace directory path
+        workspace_fixed: If True, /new keeps the same workspace directory
+        mode: Workspace mode ('daemon' or 'run'), displayed in banner
+        model: Model name to display in banner
+        provider: LLM provider name to display in banner
     """
     thread_id = str(uuid.uuid4())
-    print_banner(thread_id, workspace_dir)
+    from .EvoScientist import MEMORY_DIR
+    memory_dir = MEMORY_DIR
+    print_banner(thread_id, workspace_dir, memory_dir, mode, model, provider)
 
     history_file = str(os.path.expanduser("~/.EvoScientist_history"))
     session = PromptSession(
@@ -1408,22 +254,40 @@ def cmd_interactive(agent: Any, show_thinking: bool = True, workspace_dir: str |
                 break
 
             if user_input.lower() == "/new":
-                # New session: new workspace, new agent, new thread
-                workspace_dir = _create_session_workspace()
+                # New session: new thread; workspace only changes if not fixed
+                if not workspace_fixed:
+                    workspace_dir = _create_session_workspace()
                 console.print("[dim]Loading new session...[/dim]")
                 agent = _load_agent(workspace_dir=workspace_dir)
                 thread_id = str(uuid.uuid4())
                 console.print(f"[green]New session:[/green] [yellow]{thread_id}[/yellow]")
-                console.print(f"[dim]Workspace:[/dim] [cyan]{workspace_dir}[/cyan]\n")
+                if workspace_dir:
+                    console.print(f"[dim]Workspace:[/dim] [cyan]{_shorten_path(workspace_dir)}[/cyan]\n")
                 continue
 
             if user_input.lower() == "/thread":
                 console.print(f"[dim]Thread:[/dim] [yellow]{thread_id}[/yellow]")
                 if workspace_dir:
-                    console.print(f"[dim]Workspace:[/dim] [cyan]{workspace_dir}[/cyan]")
+                    console.print(f"[dim]Workspace:[/dim] [cyan]{_shorten_path(workspace_dir)}[/cyan]")
+                if memory_dir:
+                    console.print(f"[dim]Memory dir:[/dim] [cyan]{_shorten_path(memory_dir)}[/cyan]")
                 console.print()
                 continue
 
+            if user_input.lower() == "/skills":
+                _cmd_list_skills()
+                continue
+
+            if user_input.lower().startswith("/install-skill"):
+                source = user_input[len("/install-skill"):].strip()
+                _cmd_install_skill(source)
+                continue
+
+            if user_input.lower().startswith("/uninstall-skill"):
+                name = user_input[len("/uninstall-skill"):].strip()
+                _cmd_uninstall_skill(name)
+                continue
+
             # Stream agent response
             console.print()
             _run_streaming(agent, user_input, thread_id, show_thinking, interactive=True)
@@ -1433,7 +297,13 @@ def cmd_interactive(agent: Any, show_thinking: bool = True, workspace_dir: str |
             console.print("\n[dim]Goodbye![/dim]")
             break
         except Exception as e:
-            console.print(f"[red]Error: {e}[/red]")
+            error_msg = str(e)
+            if "authentication" in error_msg.lower() or "api_key" in error_msg.lower():
+                console.print("[red]Error: API key not configured.[/red]")
+                console.print("[dim]Run [bold]EvoSci onboard[/bold] to set up your API key.[/dim]")
+                break
+            else:
+                console.print(f"[red]Error: {e}[/red]")
 
 
 def cmd_run(agent: Any, prompt: str, thread_id: str | None = None, show_thinking: bool = True, workspace_dir: str | None = None) -> None:
@@ -1455,24 +325,30 @@ def cmd_run(agent: Any, prompt: str, thread_id: str | None = None, show_thinking
     console.print(sep)
     console.print(f"[dim]Thread: {thread_id}[/dim]")
     if workspace_dir:
-        console.print(f"[dim]Workspace: {workspace_dir}[/dim]")
+        console.print(f"[dim]Workspace: {_shorten_path(workspace_dir)}[/dim]")
     console.print()
 
     try:
         _run_streaming(agent, prompt, thread_id, show_thinking, interactive=False)
     except Exception as e:
-        console.print(f"[red]Error: {e}[/red]")
-        raise
+        error_msg = str(e)
+        if "authentication" in error_msg.lower() or "api_key" in error_msg.lower():
+            console.print("[red]Error: API key not configured.[/red]")
+            console.print("[dim]Run [bold]EvoSci onboard[/bold] to set up your API key.[/dim]")
+            raise typer.Exit(1)
+        else:
+            console.print(f"[red]Error: {e}[/red]")
+            raise
 
 
 # =============================================================================
-# Entry point
+# Agent loading helpers
 # =============================================================================
 
 def _create_session_workspace() -> str:
     """Create a per-session workspace directory and return its path."""
     session_id = datetime.now().strftime("%Y%m%d_%H%M%S")
-    workspace_dir = os.path.join(".", "workspace", session_id)
+    workspace_dir = str(new_run_dir(session_id))
     os.makedirs(workspace_dir, exist_ok=True)
     return workspace_dir
 
@@ -1487,66 +363,305 @@ def _load_agent(workspace_dir: str | None = None):
     return create_cli_agent(workspace_dir=workspace_dir)
 
 
-def main():
-    """CLI entry point."""
-    parser = argparse.ArgumentParser(
-        description="EvoScientist Agent - AI-powered research & code execution CLI",
-        formatter_class=argparse.RawDescriptionHelpFormatter,
-        epilog="""
-Examples:
-  # Interactive mode (default)
-  python -m EvoScientist --interactive
-
-  # Single-shot query
-  python -m EvoScientist "What is quantum computing?"
-
-  # Resume a conversation thread
-  python -m EvoScientist --thread-id <uuid> "Follow-up question"
-
-  # Disable thinking display
-  python -m EvoScientist --no-thinking "Your query"
-""",
-    )
+# =============================================================================
+# Typer app
+# =============================================================================
+
+app = typer.Typer(no_args_is_help=False, add_completion=False)
+
+# Config subcommand group
+config_app = typer.Typer(help="Configuration management commands", invoke_without_command=True)
+app.add_typer(config_app, name="config")
+
+
+# =============================================================================
+# Onboard command
+# =============================================================================
+
+@app.command()
+def onboard(
+    skip_validation: bool = typer.Option(
+        False,
+        "--skip-validation",
+        help="Skip API key validation during setup"
+    ),
+):
+    """Interactive setup wizard for EvoScientist.
+
+    Guides you through configuring API keys, model selection,
+    workspace settings, and agent parameters.
+    """
+    from .onboard import run_onboard
+    run_onboard(skip_validation=skip_validation)
+
+
+# =============================================================================
+# Config commands
+# =============================================================================
+
+@config_app.callback(invoke_without_command=True)
+def config_callback(ctx: typer.Context):
+    """Configuration management commands."""
+    if ctx.invoked_subcommand is None:
+        config_list()
 
-    parser.add_argument(
-        "prompt",
-        nargs="?",
-        help="Query to execute (single-shot mode)",
-    )
-    parser.add_argument(
-        "-i", "--interactive",
-        action="store_true",
-        help="Interactive conversation mode",
-    )
-    parser.add_argument(
-        "--thread-id",
-        type=str,
-        default=None,
-        help="Thread ID for conversation persistence (resume session)",
-    )
-    parser.add_argument(
-        "--no-thinking",
-        action="store_true",
-        help="Disable thinking display",
-    )
 
-    args = parser.parse_args()
-    show_thinking = not args.no_thinking
+@config_app.command("list")
+def config_list():
+    """List all configuration values."""
+    from .config import list_config, get_config_path
 
-    # Create per-session workspace
-    workspace_dir = _create_session_workspace()
+    config_data = list_config()
+
+    table = Table(title="EvoScientist Configuration", show_header=True)
+    table.add_column("Setting", style="cyan")
+    table.add_column("Value")
+
+    # Mask API keys
+    def format_value(key: str, value: Any) -> str:
+        if "api_key" in key and value:
+            return "***" + str(value)[-4:] if len(str(value)) > 4 else "***"
+        if value == "":
+            return "[dim](not set)[/dim]"
+        return str(value)
+
+    for key, value in config_data.items():
+        table.add_row(key, format_value(key, value))
+
+    console.print(table)
+    console.print(f"\n[dim]Config file: {get_config_path()}[/dim]")
+
+
+@config_app.command("get")
+def config_get(key: str = typer.Argument(..., help="Configuration key to get")):
+    """Get a single configuration value."""
+    from .config import get_config_value
+
+    value = get_config_value(key)
+    if value is None:
+        console.print(f"[red]Unknown key: {key}[/red]")
+        raise typer.Exit(1)
+
+    # Mask API keys
+    if "api_key" in key and value:
+        display_value = "***" + str(value)[-4:] if len(str(value)) > 4 else "***"
+    elif value == "":
+        display_value = "(not set)"
+    else:
+        display_value = str(value)
+
+    console.print(f"[cyan]{key}[/cyan]: {display_value}")
+
+
+@config_app.command("set")
+def config_set(
+    key: str = typer.Argument(..., help="Configuration key to set"),
+    value: str = typer.Argument(..., help="New value"),
+):
+    """Set a single configuration value."""
+    from .config import set_config_value
+
+    if set_config_value(key, value):
+        console.print(f"[green]Set {key}[/green]")
+    else:
+        console.print(f"[red]Invalid key: {key}[/red]")
+        raise typer.Exit(1)
+
+
+@config_app.command("reset")
+def config_reset(
+    yes: bool = typer.Option(False, "--yes", "-y", help="Skip confirmation prompt"),
+):
+    """Reset configuration to defaults."""
+    from .config import reset_config, get_config_path
+
+    config_path = get_config_path()
+
+    if not config_path.exists():
+        console.print("[yellow]No config file to reset.[/yellow]")
+        return
+
+    if not yes:
+        confirm = typer.confirm("Reset configuration to defaults?")
+        if not confirm:
+            console.print("[dim]Cancelled.[/dim]")
+            return
+
+    reset_config()
+    console.print("[green]Configuration reset to defaults.[/green]")
+
+
+@config_app.command("path")
+def config_path():
+    """Show the configuration file path."""
+    from .config import get_config_path
+
+    path = get_config_path()
+    exists = path.exists()
+    status = "[green]exists[/green]" if exists else "[dim]not created yet[/dim]"
+    console.print(f"{path} ({status})")
+
+
+# =============================================================================
+# Main callback (default behavior)
+# =============================================================================
+
+@app.callback(invoke_without_command=True)
+def _main_callback(
+    ctx: typer.Context,
+    prompt: Optional[str] = typer.Option(None, "-p", "--prompt", help="Query to execute (single-shot mode)"),
+    thread_id: Optional[str] = typer.Option(None, "--thread-id", help="Thread ID for conversation persistence"),
+    no_thinking: bool = typer.Option(False, "--no-thinking", help="Disable thinking display"),
+    workdir: Optional[str] = typer.Option(None, "--workdir", help="Override workspace directory for this session"),
+    use_cwd: bool = typer.Option(False, "--use-cwd", help="Use current working directory as workspace"),
+    mode: Optional[str] = typer.Option(
+        None,
+        "--mode",
+        help="Workspace mode: 'daemon' (persistent, default) or 'run' (isolated per-session)"
+    ),
+):
+    """EvoScientist Agent - AI-powered research & code execution CLI."""
+    # If a subcommand was invoked, don't run the default behavior
+    if ctx.invoked_subcommand is not None:
+        return
+
+    from dotenv import load_dotenv, find_dotenv  # type: ignore[import-untyped]
+    # find_dotenv() traverses up the directory tree to locate .env
+    load_dotenv(find_dotenv(), override=True)
+
+    # Load and apply configuration
+    from .config import get_effective_config, apply_config_to_env
+
+    # Build CLI overrides dict
+    cli_overrides = {}
+    if mode:
+        cli_overrides["default_mode"] = mode
+    if workdir:
+        cli_overrides["default_workdir"] = workdir
+    if no_thinking:
+        cli_overrides["show_thinking"] = False
+
+    config = get_effective_config(cli_overrides)
+    apply_config_to_env(config)
+
+    show_thinking = config.show_thinking if not no_thinking else False
+
+    # Validate mutually exclusive options
+    if workdir and use_cwd:
+        raise typer.BadParameter("Use either --workdir or --use-cwd, not both.")
+
+    if mode and (workdir or use_cwd):
+        raise typer.BadParameter("--mode cannot be combined with --workdir or --use-cwd")
+
+    if mode and mode not in ("run", "daemon"):
+        raise typer.BadParameter("--mode must be 'run' or 'daemon'")
+
+    ensure_dirs()
+
+    # Resolve effective mode from config (CLI mode already applied via overrides)
+    effective_mode: str | None = None  # None means explicit --workdir/--use-cwd was used
+
+    # Resolve workspace directory for this session
+    # Priority: --use-cwd > --workdir > --mode (explicit) > default_workdir > default_mode
+    if use_cwd:
+        workspace_dir = os.getcwd()
+        workspace_fixed = True
+    elif workdir:
+        workspace_dir = os.path.abspath(os.path.expanduser(workdir))
+        os.makedirs(workspace_dir, exist_ok=True)
+        workspace_fixed = True
+    elif mode:
+        # Explicit --mode overrides default_workdir
+        effective_mode = mode
+        workspace_root = config.default_workdir or str(default_workspace_dir())
+        workspace_root = os.path.abspath(os.path.expanduser(workspace_root))
+        if effective_mode == "run":
+            session_id = datetime.now().strftime("%Y%m%d_%H%M%S")
+            workspace_dir = os.path.join(workspace_root, "runs", session_id)
+            os.makedirs(workspace_dir, exist_ok=True)
+            workspace_fixed = False
+        else:  # daemon
+            workspace_dir = workspace_root
+            os.makedirs(workspace_dir, exist_ok=True)
+            workspace_fixed = True
+    elif config.default_workdir:
+        # Use configured default workdir with configured mode
+        workspace_root = os.path.abspath(os.path.expanduser(config.default_workdir))
+        effective_mode = config.default_mode
+        if effective_mode == "run":
+            session_id = datetime.now().strftime("%Y%m%d_%H%M%S")
+            workspace_dir = os.path.join(workspace_root, "runs", session_id)
+            os.makedirs(workspace_dir, exist_ok=True)
+            workspace_fixed = False
+        else:  # daemon
+            workspace_dir = workspace_root
+            os.makedirs(workspace_dir, exist_ok=True)
+            workspace_fixed = True
+    else:
+        effective_mode = config.default_mode
+        if effective_mode == "run":
+            workspace_dir = _create_session_workspace()
+            workspace_fixed = False
+        else:  # daemon mode (default)
+            workspace_dir = str(default_workspace_dir())
+            os.makedirs(workspace_dir, exist_ok=True)
+            workspace_fixed = True
 
     # Load agent with session workspace
     console.print("[dim]Loading agent...[/dim]")
     agent = _load_agent(workspace_dir=workspace_dir)
 
-    if args.interactive:
-        cmd_interactive(agent, show_thinking=show_thinking, workspace_dir=workspace_dir)
-    elif args.prompt:
-        cmd_run(agent, args.prompt, thread_id=args.thread_id, show_thinking=show_thinking, workspace_dir=workspace_dir)
+    if prompt:
+        # Single-shot mode: execute query and exit
+        cmd_run(agent, prompt, thread_id=thread_id, show_thinking=show_thinking, workspace_dir=workspace_dir)
     else:
-        # Default: interactive mode
-        cmd_interactive(agent, show_thinking=show_thinking, workspace_dir=workspace_dir)
+        # Interactive mode (default)
+        cmd_interactive(
+            agent,
+            show_thinking=show_thinking,
+            workspace_dir=workspace_dir,
+            workspace_fixed=workspace_fixed,
+            mode=effective_mode,
+            model=config.model,
+            provider=config.provider,
+        )
+
+
+def _configure_logging():
+    """Configure logging with warning symbols for better visibility."""
+    from rich.logging import RichHandler
+
+    class DimWarningHandler(RichHandler):
+        """Custom handler that renders warnings in dim style."""
+
+        def emit(self, record: logging.LogRecord) -> None:
+            if record.levelno == logging.WARNING:
+                # Use Rich console to print dim warning
+                msg = record.getMessage()
+                console.print(f"[dim yellow]\u26a0\ufe0f  Warning:[/dim yellow] [dim]{msg}[/dim]")
+            else:
+                super().emit(record)
+
+    # Configure root logger to use our handler for WARNING and above
+    handler = DimWarningHandler(console=console, show_time=False, show_path=False, show_level=False)
+    handler.setLevel(logging.WARNING)
+
+    # Apply to root logger (catches all loggers including deepagents)
+    root_logger = logging.getLogger()
+    # Remove existing handlers to avoid duplicate output
+    for h in root_logger.handlers[:]:
+        root_logger.removeHandler(h)
+    root_logger.addHandler(handler)
+    root_logger.setLevel(logging.WARNING)
+
+
+def main():
+    """CLI entry point — delegates to the Typer app."""
+    import warnings
+    warnings.filterwarnings("ignore", message=".*not known to support tools.*")
+    warnings.filterwarnings("ignore", message=".*type is unknown and inference may fail.*")
+    _configure_logging()
+    app()
 
 
 if __name__ == "__main__":