project: bump version to 0.1.2

asyncio signal handlers freeze ContextVars at install time; reinstalling
while allow_task_cancel was still False left cancel permanently disabled.
Use a process-level prompt depth counter and reinstall only after depth=0.

CLAUDE.md

@@ -12,12 +12,20 @@ Plyngent is an LLM chat and agent toolkit (Python 3.14+, PDM-managed). Single-us
 pdm install          # first-time dependency setup
 pdm sync             # sync after pulling changes
 
-pdm run basedpyright .   # type checking (basedpyright, "recommended" strictness)
 pdm run ruff check .           # linting
-pdm run ruff format .    # formatting
+pdm run ruff format .          # apply formatting
+pdm run ruff format --check .  # CI: fail if unformatted (do not skip)
+pdm run basedpyright .         # type checking (basedpyright, "recommended" strictness)
 pdm run pytest                 # tests (pytest-asyncio auto mode)
+
+# Commit gateway (prek — https://prek.j178.dev/): ruff check/format + basedpyright
+uv tool install prek           # once
+prek install                   # wire git pre-commit hook (once per clone)
+prek run --all-files           # run all hooks on demand
 ```
 
+GitHub Actions runs `ruff check`, `ruff format --check`, `basedpyright`, then `pytest`. Local commits run the same checks via `prek.toml` so `ruff format` is not forgotten.
+
 ## Architecture
 
 ### Data modeling: `msgspec.Struct`
@@ -70,15 +78,16 @@ Async SQLAlchemy + aiosqlite. `MemoryStore`: schema init (+ lightweight SQLite `
 
 Module-level `@tool` handlers. Call `set_workspace_root()` before use.
 
-- **`workspace`**: path resolve under root; path substring denylist; command basename denylist; clearer deny messages.
-- **`file`**: `read_file`, `write_file`, `listdir`, `tree`, `glob_paths`, `grep_files` (regex, skip VCS/binary), `edit_replace`, `edit_lineno` (1-based range), `copy_path` / `move_path` / `delete_path`.
-- **`process`**: `run_command` (argv, no shell, timeout, optional stdin/env); PTY `open_pty` / `read_pty` / `write_pty` / `close_pty` (POSIX: `pty`+`fork`; Windows: ConPTY via `pywinpty` env marker dep).
-- PTY: backend in `pty_backend.py`; structured status (`alive`/`exit_code`/`data`); `read_pty(..., until=)`; session limit/idle TTL/output budget; close terminate→kill.
+- **`workspace`**: path resolve under primary root **or** temporary allowlist roots; path substring denylist; command basename denylist; clearer deny messages.
+- **`file`**: `read_file` (`with_lineno`), `write_file`, `listdir`, `tree` (VCS + default noise dirs + optional `skip_dirs` / denylist walk), `glob_paths`, `grep_files` (regex, skip VCS/binary), `edit_replace`, `edit_lineno` (1-based range), `copy_path` / `move_path` / `delete_path`, `new_temporary_workspace` (system temp allowlist; cleanup on chat exit; no session rebind).
+- **`process`**: `run_command` (argv, no shell, timeout, optional stdin/env); PTY `open_pty` / `read_pty` / `write_pty` (literal) / `write_pty_keys` (escapes) / `close_pty` (POSIX: `pty`+`fork`; Windows: ConPTY via `pywinpty` env marker dep).
+- PTY: backend in `pty_backend.py`; structured status (`alive`/`exit_code`/`data`); `read_pty(..., until=)` (**CSI sanitized** so host TTY is never reset); keys via `write_pty_keys` only (`\xHH`, `ctrl+x`, `key=esc`); session limit/idle TTL/output budget; close terminate→kill.
 - CLI limit hooks: interactive confirm to raise tool-loop rounds, PTY session cap, or PTY output budget.
-- Destructive confirms: `classify_danger` + `ToolRegistry(on_confirm=…)`; CLI default deny; config `confirm_destructive` / `path_denylist`. Session YOLO: `/yolo on|off|once` and `--yes` (skip soft confirms; hard denylists unchanged; `once` expires after the next user turn).
+- Destructive confirms: `classify_danger` + `ToolRegistry(on_confirm=…)`; CLI default deny; config `confirm_destructive` / `path_denylist`. Soft confirm also for shells/REPLs and `python|bash -c` one-liners (argv + code preview); deny may include a user comment for the model. Session YOLO: `/yolo on|off|once` and `--yes` (skip soft confirms; hard denylists unchanged; `once` expires after the next user turn).
 - **`vcs`**: read-only VCS tools (`vcs_kind` / `vcs_status` / `vcs_diff` / `vcs_log` / `vcs_branch`) via `VcsBackend` protocol; **git** implemented; detectors are pluggable for other systems.
 - **`chat`**: human prompts as tools — `ask_user_line` / `ask_user_choice` / `ask_user_form` (shared `prompting` core).
-- **`DEFAULT_TOOLS`**: file + process + vcs + chat tool list for a `ToolRegistry`.
+- **`todo`**: LIFO stack of **task groups** (not a queue of tasks) — `todo_push` creates one group of siblings; `todo_pop` removes the whole top group; `todo_update` by id; DFS breakdown push[T1,T2]→push[T1.1…]→pop→push[T2.1…]; stored on session row; agent injects a developer review message if open todos and no todo tool use in the turn.
+- **`DEFAULT_TOOLS`**: file + process + vcs + chat + todo tool list for a `ToolRegistry`.
 
 ### Prompting (`prompting.py`)
 
@@ -89,7 +98,7 @@ Shared interactive I/O: `ask` / `choose` / `form` / `confirm` with pluggable bac
 Click app + readline REPL. Entry: `plyngent` / `python -m plyngent`.
 
 - **`plyngent chat`**: provider/model (flags or interactive; Tab via readline in `prompting`); sessions store `provider_name`/`model` and restore on resume; SQLite via `[database]` (file DB under user data if unset/`:memory:`); workspace-bound; resume latest for cwd/`--workspace` by default (`--new` / `--session`). One-shot: `-p/--prompt` and non-TTY stdin; exit codes 0/1/2/3; `--yes` (YOLO on), `--stream/--no-stream`, `--quiet`. Root `--log-level`.
-- Slash: Click group in `cli/slash.py` + `awaitlet` for async work; Tab completer from registry + ParamType `shell_complete`. Multiline `"""` … `"""`; `/edit` via `$EDITOR`. `/yolo on|off|once` for soft destructive confirms.
+- Slash: Click group in `cli/slash.py` + `awaitlet` for async work; Tab completer from registry + ParamType `shell_complete`. Multiline `"""` … `"""`; `/edit` via `$EDITOR`. `/yolo on|off|once` for soft destructive confirms. `/model --persist` / `/models --persist` write model catalog entries into TOML. `/todos` for human show/push/pop/clear of the todo stack.
 - Explicit `/resume` or `--session` from another workspace prompts: **keep** / **update** / **abort**.
 - Failed/cancelled turns: user kept; **committed tool rounds kept** (side effects not re-run on `/retry`); only unfinished assistant rolled back; Ctrl+C cancels; TTY confirms off-loop; auto-retry 10s/20s/30s then `/retry`.
 - **`plyngent providers`**, **`config path|edit`**. No providers + `$EDITOR` → optional edit then reload.

README.md

@@ -62,15 +62,25 @@ pdm sync             # after pull
 pdm run plyngent --help
 ```
 
-Dev checks:
+Dev checks (same order as CI):
 
 ```bash
-pdm run basedpyright .
 pdm run ruff check .
-pdm run ruff format .
+pdm run ruff format --check .   # or: pdm run ruff format .  to apply
+pdm run basedpyright .
 pdm run pytest
 ```
 
+**Commit gateway** ([prek](https://prek.j178.dev/)): runs ruff check + format and basedpyright on `git commit` so format is not forgotten.
+
+```bash
+uv tool install prek    # once
+prek install            # once per clone (installs .git/hooks/pre-commit)
+prek run --all-files    # run all hooks on demand
+```
+
+Config: `prek.toml`. CI still runs the same checks in GitHub Actions.
+
 ## Basic usage
 
 ```bash
@@ -186,7 +196,8 @@ Type `/help` in the REPL for the live list. Common ones:
 | Command | Purpose |
 |---------|---------|
 | `/status` | Provider, session, context/usage estimates |
-| `/history [n]` | Recent messages |
+| `/history [n\|last]` | Recent messages (default preview; `last`/`1` = full + markdown) |
+| `/history --full` | Full bodies for the selected window |
 | `/sessions` | Sessions for this workspace |
 | `/new` `/resume` `/rename` `/delete` | Session lifecycle (`/delete` confirms) |
 | `/export [md\|json] [path]` | Transcript from DB (no secrets) |
@@ -196,7 +207,10 @@ Type `/help` in the REPL for the live list. Common ones:
 
 | `/retry` | Re-run incomplete last user turn (after error/cancel) |
 | `/provider` `/model` | Switch without restarting |
-| `/models` | List config + remote `GET /models` (`--refresh` bypasses cache) |
+| `/model --persist` | Save current model id into `plyngent.toml` catalog |
+| `/models` | List config + remote `GET /models` (always re-fetches) |
+| `/models --persist` | Merge remote catalog into TOML for this provider |
+| `/todos` | Todo/task stack: list, push, pop, done, clear |
 | `/config` | Edit `plyngent.toml` in `$EDITOR` and reload |
 | `/quit` | Leave the REPL |
 
@@ -210,14 +224,17 @@ User messages are saved immediately. On API error or Ctrl+C, partial assistant/t
 
 ## Tools (when enabled)
 
-Default registry: file ops, `run_command` / PTY (POSIX openpty; Windows ConPTY via pywinpty), read-only VCS (git), and human prompts (`ask_user_line` / `ask_user_choice` / `ask_user_form`).
+Default registry: file ops (including `tree` with default noise-dir skips), `run_command` / PTY (POSIX openpty; Windows ConPTY via pywinpty), read-only VCS (git), human prompts (`ask_user_line` / `ask_user_choice` / `ask_user_form`), and todo stack tools (`todo_list` / `todo_push` / `todo_pop` / `todo_update` / `todo_clear`).
 
 Safety defaults:
 
-- Paths stay under the workspace; optional `path_denylist` substrings.
+- Paths stay under the workspace; optional `path_denylist` substrings (`tree` also skips denylisted children by default).
 - Command basename denylist (e.g. dangerous shells/utilities).
 - Destructive tools (delete/move/overwrite) can require confirm (`confirm_destructive`; default deny in non-TTY). Override for the session with `/yolo on|off|once` or startup `--yes` (path/command denylists still apply).
 - PTY sessions: caps, idle TTL, output budget; master FD is non-inheritable; sessions closed on chat exit.
+  Prefer file tools over full-screen editors (`vim`/`nano`) for edits. `read_pty` sanitizes CSI/controls
+  so tool results cannot reprogram the host TTY (no host terminal reset on exit).
+  `write_pty` is literal text only; use `write_pty_keys` for `\xHH`, `ctrl+x`, `key=esc|enter|…`.
 
 ## Usage / context (CLI)
 

doc/development-principles.md

@@ -45,7 +45,10 @@ Then for every projects, check the dev dependency group where you can find tools
 
 Type checking: `pdm run basedpyright .`
 Linting: `pdm run ruff check .`
-Formating: `pdm run ruff format .`
+Formatting (apply): `pdm run ruff format .`
+Formatting (CI check): `pdm run ruff format --check .`
+
+CI (`.github/workflows/ci.yml`) runs lint, **format check**, typecheck, then tests. Always run `pdm run ruff format .` before push so `ruff format --check` does not fail on `main` after a release tag has already published.
 
 <!-- Contents in comments are for projects with long-period developments, but this is a new project.
 

prek.toml

@@ -0,0 +1,27 @@
+# Commit gateway via prek (https://prek.j178.dev/) — drop-in pre-commit compatible.
+# Install: uv tool install prek  (or: pipx install prek)
+# Wire git: prek install
+# Manual:  prek run --all-files
+
+default_install_hook_types = ["pre-commit"]
+default_stages = ["pre-commit"]
+default_language_version = { python = "python3.14" }
+
+# Ruff: lint (with autofix) then format — order matters (fix before format).
+# https://docs.astral.sh/ruff/integrations/#pre-commit
+[[repos]]
+repo = "https://github.com/astral-sh/ruff-pre-commit"
+rev = "v0.15.22"
+hooks = [
+  { id = "ruff-check", args = ["--fix"], types_or = ["python", "pyi"] },
+  { id = "ruff-format", types_or = ["python", "pyi"] },
+]
+
+# basedpyright: full-project typecheck (same as CI `pdm run basedpyright .`).
+# Mirror hook: https://docs.basedpyright.com/latest/installation/prek-hook/
+# Uses system+PDM so imports resolve from the project venv (isolated hook envs lack deps).
+[[repos]]
+repo = "local"
+hooks = [
+  { id = "basedpyright", name = "basedpyright", language = "system", entry = "pdm run basedpyright .", pass_filenames = false, files = "\\.pyi?$" },
+]

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "plyngent"
-version = "0.1.1"
+version = "0.1.2"
 description = "LLM chat and agent toolkit"
 authors = [
   { name = "HivertMoZara", email = "worldmozara@163.com" },

src/plyngent/agent/chat.py

@@ -29,6 +29,7 @@ if TYPE_CHECKING:
 
     from .client import ChatClient
     from .events import AgentEvent
+    from .todo_stack import TodoStack
     from .tools import ToolRegistry
 
     type LimitContinueHook = Callable[[str], bool | Awaitable[bool]]
@@ -118,6 +119,7 @@ class ChatAgent:
     max_tool_result_chars: int
     parallel_tools: bool
     max_context_tokens: int
+    todo_stack: TodoStack | None
     messages: list[AnyChatMessage]
     session_usage: TokenUsage
     last_turn_usage: TokenUsage
@@ -143,6 +145,7 @@ class ChatAgent:
         max_tool_result_chars: int = DEFAULT_TOOL_RESULT_MAX_CHARS,
         parallel_tools: bool = True,
         max_context_tokens: int = DEFAULT_CONTEXT_MAX_TOKENS,
+        todo_stack: TodoStack | None = None,
     ) -> None:
         self.client = client
         self.model = model
@@ -157,6 +160,7 @@ class ChatAgent:
         self.max_tool_result_chars = max_tool_result_chars
         self.parallel_tools = parallel_tools
         self.max_context_tokens = max_context_tokens
+        self.todo_stack = todo_stack
         self.messages = list(messages) if messages is not None else []
         self.session_usage = TokenUsage()
         self.last_turn_usage = TokenUsage()
@@ -200,14 +204,38 @@ class ChatAgent:
         if self._persist_from == 0:
             self._persist_from = 1
 
+    def replace_messages(
+        self,
+        messages: Sequence[AnyChatMessage],
+        *,
+        persisted: bool = True,
+        persist_from: int | None = None,
+    ) -> None:
+        """Replace in-memory history and align the persistence checkpoint.
+
+        When *persist_from* is set, it is used as the checkpoint cursor
+        (clamped to ``[0, len(messages)]``). Otherwise *persisted* true means
+        all messages are already stored; false means none are.
+        """
+        self.messages = list(messages)
+        if persist_from is not None:
+            self._persist_from = max(0, min(persist_from, len(self.messages)))
+        else:
+            self._persist_from = len(self.messages) if persisted else 0
+        self._ensure_system_prompt()
+
+    @property
+    def persist_from(self) -> int:
+        """Index of the first unpersisted message (checkpoint cursor)."""
+        return self._persist_from
+
     async def load_history(self) -> None:
         """Replace in-memory messages from the bound memory session."""
         if self.memory is None or self.session_id is None:
             msg = "load_history requires memory and session_id"
             raise RuntimeError(msg)
-        self.messages = await self.memory.list_messages(self.session_id)
-        self._persist_from = len(self.messages)
-        self._ensure_system_prompt()
+        loaded = await self.memory.list_messages(self.session_id)
+        self.replace_messages(loaded, persisted=True)
 
     async def bind_session(self, session_id: int, *, load: bool = True) -> None:
         """Attach a memory session id; optionally load existing messages."""
@@ -265,6 +293,8 @@ class ChatAgent:
         side-effecting tools. Unfinished assistant/stream suffix is rolled back.
         """
         user_index = self._user_index(user_msg)
+        if self.todo_stack is not None:
+            self.todo_stack.begin_turn()
 
         completed = False
         turn_usage = TokenUsage()
@@ -283,6 +313,7 @@ class ChatAgent:
                 max_tool_result_chars=self.max_tool_result_chars,
                 parallel_tools=self.parallel_tools,
                 max_context_tokens=self.max_context_tokens,
+                todo_stack=self.todo_stack,
             ):
                 if isinstance(event, UsageEvent):
                     turn_rounds += 1

src/plyngent/agent/compact.py

@@ -8,8 +8,8 @@ from plyngent.lmproto.openai_compatible.model import (
     AssistantChatMessage,
     AssistantFunctionToolCall,
     ChatCompletionsParam,
+    DeveloperChatMessage,
     SystemChatMessage,
-    ToolChatMessage,
     UserChatMessage,
 )
 
@@ -49,6 +49,8 @@ def format_transcript(messages: Sequence[AnyChatMessage]) -> str:
     for msg in messages:
         if isinstance(msg, SystemChatMessage):
             lines.append(f"[system] {msg.content}")
+        elif isinstance(msg, DeveloperChatMessage):
+            lines.append(f"[developer] {msg.content}")
         elif isinstance(msg, UserChatMessage):
             lines.append(f"[user] {msg.content}")
         elif isinstance(msg, AssistantChatMessage):
@@ -62,10 +64,9 @@ def format_transcript(messages: Sequence[AnyChatMessage]) -> str:
                         lines.append(f"[assistant tool_call] {call.function.name}({call.function.arguments})")
                     else:
                         lines.append(f"[assistant tool_call] custom id={call.id}")
-        elif isinstance(msg, ToolChatMessage):
-            lines.append(f"[tool {msg.tool_call_id}] {msg.content}")
         else:
-            lines.append(f"[message] {msg!r}")
+            # ToolChatMessage (remaining AnyChatMessage arm)
+            lines.append(f"[tool {msg.tool_call_id}] {msg.content}")
     return "\n".join(lines)
 
 

src/plyngent/agent/loop.py

@@ -13,6 +13,7 @@ from plyngent.lmproto.openai_compatible.model import (
     AssistantChatMessage,
     AssistantFunctionToolCall,
     ChatCompletionsParam,
+    DeveloperChatMessage,
     StreamOptions,
     StreamToolCallDelta,
     ToolChatMessage,
@@ -45,6 +46,7 @@ if TYPE_CHECKING:
     from plyngent.lmproto.openai_compatible.model import AnyChatMessage, AnyToolItem
 
     from .client import ChatClient
+    from .todo_stack import TodoStack
     from .tools import ToolRegistry
 
     type LimitContinueHook = Callable[[str], bool | Awaitable[bool]]
@@ -114,6 +116,66 @@ async def _execute_tool_calls(
         yield ToolResultEvent(message=tool_msg)
 
 
+def _assistant_has_payload(assistant: AssistantChatMessage) -> bool:
+    """True if the model produced text, reasoning, or tool calls."""
+    if assistant.tool_calls is not UNSET and assistant.tool_calls:
+        return True
+    if isinstance(assistant.content, str) and assistant.content.strip():
+        return True
+    reasoning = assistant.reasoning_content
+    return bool(isinstance(reasoning, str) and reasoning.strip())
+
+
+def _finish_reason_value(finish: object) -> str | None:
+    if finish is UNSET or finish is None:
+        return None
+    if isinstance(finish, str) and finish.strip():
+        return finish.strip()
+    return None
+
+
+def _validate_assistant_terminal(
+    assistant: AssistantChatMessage,
+    *,
+    finish_reason: str | None,
+    stream_terminal: bool,
+) -> None:
+    """Raise when the round is not a usable agent stop.
+
+    Distinguishes empty generation, truncated/filtered stops, and missing
+    stream terminals (network/client glitch) from a normal stop/tool_calls end.
+    """
+    reason = (finish_reason or "").lower() or None
+
+    if reason in {"length", "content_filter"}:
+        label = "truncated (max tokens)" if reason == "length" else "content filter"
+        detail = ""
+        if isinstance(assistant.content, str) and assistant.content.strip():
+            detail = f"; partial text kept ({len(assistant.content)} chars)"
+        msg = f"model stopped early: {label}{detail}"
+        raise RuntimeError(msg)
+
+    if reason in {"failed", "incomplete", "cancelled"}:
+        msg = f"model response status: {reason}"
+        raise RuntimeError(msg)
+
+    if _assistant_has_payload(assistant):
+        return
+
+    if not stream_terminal and reason is None:
+        msg = (
+            "stream ended without a terminal signal (no finish_reason / response.completed) and empty assistant output"
+        )
+        raise RuntimeError(msg)
+
+    if reason in {"stop", "tool_calls", "function_call"} or reason is None:
+        msg = "empty model completion (no text, reasoning, or tool calls)"
+        raise RuntimeError(msg)
+
+    msg = f"empty model completion (finish_reason={reason})"
+    raise RuntimeError(msg)
+
+
 async def _non_stream_round(
     client: ChatClient,
     param: ChatCompletionsParam,
@@ -122,7 +184,14 @@ async def _non_stream_round(
     if not response.choices:
         msg = "chat completion response contained no choices"
         raise RuntimeError(msg)
-    assistant = response.choices[0].message
+    choice = response.choices[0]
+    assistant = choice.message
+    finish = _finish_reason_value(choice.finish_reason)
+    _validate_assistant_terminal(
+        assistant,
+        finish_reason=finish,
+        stream_terminal=True,
+    )
     reasoning = assistant.reasoning_content
     if isinstance(reasoning, str) and reasoning:
         yield ReasoningDeltaEvent(content=reasoning)
@@ -154,6 +223,8 @@ async def _stream_round(
     reasoning_parts: list[str] = []
     tool_deltas: list[StreamToolCallDelta] = []
     last_api_usage: object = UNSET
+    finish_reason: str | None = None
+    saw_terminal = False
 
     async for chunk in stream:
         parsed = token_usage_from_api(chunk.usage)
@@ -162,6 +233,10 @@ async def _stream_round(
         if not chunk.choices:
             continue
         choice = chunk.choices[0]
+        fr = _finish_reason_value(choice.finish_reason)
+        if fr is not None:
+            finish_reason = fr
+            saw_terminal = True
         delta = choice.delta
         if isinstance(delta.reasoning_content, str) and delta.reasoning_content:
             reasoning_parts.append(delta.reasoning_content)
@@ -185,6 +260,16 @@ async def _stream_round(
         tool_calls=tool_calls,
         reasoning_content=full_reasoning or UNSET,
     )
+    # Usage-only final chunks leave choices empty; a non-empty usage after
+    # content still is not a finish_reason. Prefer explicit finish_reason.
+    # If we got payload but no finish_reason, treat as terminal (some providers
+    # omit it); if empty and no finish_reason, flag as missing terminal.
+    stream_terminal = saw_terminal or _assistant_has_payload(assistant)
+    _validate_assistant_terminal(
+        assistant,
+        finish_reason=finish_reason,
+        stream_terminal=stream_terminal,
+    )
     yield AssistantMessageEvent(message=assistant)
     yield UsageEvent(
         usage=resolve_round_usage(last_api_usage, param.messages, assistant),
@@ -235,6 +320,7 @@ async def run_chat_loop(
     max_tool_result_chars: int = DEFAULT_TOOL_RESULT_MAX_CHARS,
     parallel_tools: bool = True,
     max_context_tokens: int = DEFAULT_CONTEXT_MAX_TOKENS,
+    todo_stack: TodoStack | None = None,
 ) -> AsyncIterator[AgentEvent]:
     """Multi-round chat/tool loop; mutates ``messages`` in place and yields events.
 
@@ -242,6 +328,10 @@ async def run_chat_loop(
     text deltas as chunks arrive; tool calls are merged from stream deltas.
     Multiple tool calls in one round run in parallel when ``parallel_tools``.
     Request payloads may shrink older tool results when over ``max_context_tokens``.
+
+    When *todo_stack* is set and still has open items after a natural stop with
+    no ``todo_*`` tool use this turn, injects a review user message and continues
+    once (so the model must check or update the stack).
     """
     tool_items: Sequence[AnyToolItem] | None = None
     if tools is not None and len(tools) > 0:
@@ -252,6 +342,7 @@ async def run_chat_loop(
     # Calibrate soft-compact from last model call's prompt_tokens (API preferred).
     prompt_tokens_hint: int | None = None
     sent_estimate_tokens: int | None = None
+    todo_review_injected = False
 
     while True:
         while rounds_used < allowance:
@@ -280,6 +371,11 @@ async def run_chat_loop(
             assistant = _last_assistant(messages, pre_len)
             tool_calls = assistant.tool_calls
             if tool_calls is UNSET or not tool_calls or tools is None:
+                if todo_stack is not None and todo_stack.needs_review() and not todo_review_injected:
+                    todo_review_injected = True
+                    # Non-user control identity so retry/history don't treat this as human input.
+                    messages.append(DeveloperChatMessage(content=todo_stack.review_prompt()))
+                    continue
                 return
             async for event in _execute_tool_calls(
                 tools,

src/plyngent/agent/responses_bridge.py

@@ -29,10 +29,10 @@ from plyngent.lmproto.openai_compatible.model import (
     ChatCompletionsParam,
     ChunkChoice,
     DeltaMessage,
+    DeveloperChatMessage,
     StreamFunctionDelta,
     StreamToolCallDelta,
     SystemChatMessage,
-    ToolChatMessage,
     ToolFunctionItem,
     UserChatMessage,
 )
@@ -97,21 +97,22 @@ def chat_messages_to_responses_input(
         if isinstance(message, SystemChatMessage):
             if message.content.strip():
                 instructions_parts.append(message.content)
+        elif isinstance(message, DeveloperChatMessage):
+            # Keep mid-turn control as input developer messages (not folded into instructions).
+            if message.content.strip():
+                items.append(ResponseEasyInputMessage(role="developer", content=message.content))
         elif isinstance(message, UserChatMessage):
             items.append(ResponseEasyInputMessage(role="user", content=message.content))
         elif isinstance(message, AssistantChatMessage):
             items.extend(_assistant_to_input_items(message))
-        elif isinstance(message, ToolChatMessage):
+        else:
+            # ToolChatMessage (remaining AnyChatMessage arm)
             items.append(
                 ResponseFunctionToolCallOutput(
                     call_id=message.tool_call_id,
                     output=message.content,
                 )
             )
-        else:
-            content = getattr(message, "content", None)
-            if isinstance(content, str) and content:
-                items.append(ResponseEasyInputMessage(role="user", content=content))
 
     instructions = "\n\n".join(instructions_parts) if instructions_parts else None
     return instructions, items
@@ -158,10 +159,33 @@ def _reasoning_summary_text(response: Response) -> str:
     return "".join(parts)
 
 
+def responses_status_to_finish_reason(
+    response: Response,
+    *,
+    has_tool_calls: bool,
+) -> str:
+    """Map Responses ``status`` to a chat-style finish_reason for the agent loop."""
+    status = response.status
+    status_s = status if isinstance(status, str) else None
+    if status_s == "incomplete":
+        details = response.incomplete_details
+        if details is not UNSET and details is not None:
+            raw_reason = details.reason
+            if raw_reason is not UNSET and raw_reason == "content_filter":
+                return "content_filter"
+        return "length"
+    if status_s in {"failed", "cancelled"}:
+        return status_s
+    if has_tool_calls:
+        return "tool_calls"
+    return "stop"
+
+
 def response_to_chat_completion(response: Response) -> ChatCompletionResponse:
     """Wrap Responses result as a synthetic chat completion for the agent loop."""
     assistant = response_to_assistant_message(response)
-    finish: str | None = "tool_calls" if assistant.tool_calls is not UNSET else "stop"
+    has_tools = assistant.tool_calls is not UNSET and bool(assistant.tool_calls)
+    finish = responses_status_to_finish_reason(response, has_tool_calls=has_tools)
     usage = response.usage if response.usage is not UNSET else UNSET
     created = int(response.created_at)
     return ChatCompletionResponse(
@@ -180,6 +204,28 @@ def response_to_chat_completion(response: Response) -> ChatCompletionResponse:
     )
 
 
+def finish_reason_chunk(
+    *,
+    model: str,
+    finish_reason: str,
+    created: int = 0,
+) -> ChatCompletionChunk:
+    """Terminal stream chunk carrying only ``finish_reason`` (no delta text)."""
+    return ChatCompletionChunk(
+        id="resp-stream",
+        object="chat.completion.chunk",
+        created=created,
+        model=model,
+        choices=[
+            ChunkChoice(
+                index=0,
+                delta=DeltaMessage(),
+                finish_reason=cast("Any", finish_reason),
+            )
+        ],
+    )
+
+
 def text_delta_chunk(*, model: str, content: str, created: int = 0) -> ChatCompletionChunk:
     return ChatCompletionChunk(
         id="resp-stream",

src/plyngent/agent/responses_client.py

@@ -8,8 +8,11 @@ from msgspec import UNSET
 
 from plyngent.agent.responses_bridge import (
     chat_param_to_responses_kwargs,
+    finish_reason_chunk,
     reasoning_delta_chunk,
+    response_to_assistant_message,
     response_to_chat_completion,
+    responses_status_to_finish_reason,
     text_delta_chunk,
     tool_call_chunks_from_response,
     usage_chunk_from_response,
@@ -109,9 +112,17 @@ class ResponsesChatClient:
                 except TypeError, ValueError, msgspec.ValidationError:
                     final = None
 
-        if final is not None:
+        if final is None:
+            # Stream ended without response.completed — signal missing terminal.
+            # Loop will treat empty + no finish_reason as a glitch.
+            return
+
+        assistant = response_to_assistant_message(final)
+        has_tools = assistant.tool_calls is not UNSET and bool(assistant.tool_calls)
+        finish = responses_status_to_finish_reason(final, has_tool_calls=has_tools)
         for chunk in tool_call_chunks_from_response(final, model=model):
             yield chunk
+        yield finish_reason_chunk(model=model, finish_reason=finish)
         usage = usage_chunk_from_response(final, model=model)
         if usage is not None:
             yield usage

src/plyngent/agent/todo_stack.py

@@ -0,0 +1,304 @@
+from __future__ import annotations
+
+from typing import Literal, cast
+
+import msgspec
+from msgspec import Struct, field
+
+type TodoStatus = Literal["pending", "in_progress", "done", "cancelled"]
+
+_OPEN: frozenset[str] = frozenset({"pending", "in_progress"})
+
+
+class TodoItem(Struct, omit_defaults=True):
+    """One task inside a group (siblings share a group; not stacked individually)."""
+
+    id: str
+    title: str
+    status: TodoStatus = "pending"
+    notes: str = ""
+
+
+class TodoGroup(Struct, omit_defaults=True):
+    """One stack entry: a group of sibling tasks pushed together."""
+
+    items: list[TodoItem] = field(default_factory=list)
+
+
+class TodoStackData(Struct, omit_defaults=True):
+    """LIFO of **groups**: ``groups[0]`` bottom, ``groups[-1]`` **TOP** group."""
+
+    groups: list[TodoGroup] = field(default_factory=list)
+    next_id: int = 1
+
+
+class TodoStack:
+    """LIFO stack of **task groups** (not a queue of individual tasks).
+
+    - **Push** always creates **one new group** containing one or more sibling
+      tasks (``push T1, T2`` is one frame, not two stack levels).
+    - **Pop** removes the entire **top group**.
+    - Within a group, update tasks by id (done / in_progress / …).
+
+    Breakdown pattern::
+
+        push [T1, T2]        # top group = {T1, T2}
+        push [T1.1, T1.2]    # top group = {T1.1, T1.2}; under = {T1, T2}
+        # finish T1.1 / T1.2 via update…
+        pop                  # leave child group; top again = {T1, T2}
+        push [T2.1]          # top group = {T2.1}
+    """
+
+    def __init__(self, data: TodoStackData | None = None) -> None:
+        self._data: TodoStackData = data if data is not None else TodoStackData()
+        self._touched_this_turn: bool = False
+
+    @property
+    def groups(self) -> list[TodoGroup]:
+        """Bottom → top (last is top group)."""
+        return self._data.groups
+
+    @property
+    def top_group(self) -> TodoGroup | None:
+        if not self._data.groups:
+            return None
+        return self._data.groups[-1]
+
+    @property
+    def depth(self) -> int:
+        return len(self._data.groups)
+
+    @property
+    def touched_this_turn(self) -> bool:
+        return self._touched_this_turn
+
+    def begin_turn(self) -> None:
+        self._touched_this_turn = False
+
+    def mark_touched(self) -> None:
+        self._touched_this_turn = True
+
+    def all_items(self) -> list[TodoItem]:
+        return [item for group in self._data.groups for item in group.items]
+
+    def open_items(self) -> list[TodoItem]:
+        return [item for item in self.all_items() if item.status in _OPEN]
+
+    def is_empty(self) -> bool:
+        return not self._data.groups
+
+    def needs_review(self) -> bool:
+        return bool(self.open_items()) and not self._touched_this_turn
+
+    def to_data(self) -> TodoStackData:
+        return self._data
+
+    @classmethod
+    def from_raw(cls, raw: object | None) -> TodoStack:  # noqa: C901, PLR0911
+        if raw is None or not isinstance(raw, dict):
+            return cls()
+        blob = cast("dict[str, object]", raw)
+
+        # Current shape: {groups: [...], next_id}
+        if "groups" in blob:
+            try:
+                data = msgspec.convert(raw, type=TodoStackData)
+            except msgspec.ValidationError, TypeError, ValueError:
+                return cls()
+            if data.next_id < 1:
+                data = msgspec.structs.replace(data, next_id=1)
+            return cls(data)
+
+        # Intermediate nested frames → groups (same structure).
+        if "frames" in blob:
+            try:
+                frames_raw = blob.get("frames")
+                next_raw = blob.get("next_id", 1)
+                next_id = max(1, int(next_raw) if isinstance(next_raw, int | str) else 1)
+                groups: list[TodoGroup] = []
+                if isinstance(frames_raw, list):
+                    for frame in cast("list[object]", frames_raw):
+                        if not isinstance(frame, dict):
+                            continue
+                        frame_map = cast("dict[str, object]", frame)
+                        frame_items = msgspec.convert(frame_map.get("items"), type=list[TodoItem])
+                        if frame_items:
+                            groups.append(TodoGroup(items=frame_items))
+                return cls(TodoStackData(groups=groups, next_id=next_id))
+            except msgspec.ValidationError, TypeError, ValueError:
+                return cls()
+
+        # Flat items list → one group (legacy).
+        if "items" in blob:
+            try:
+                items = msgspec.convert(blob.get("items"), type=list[TodoItem])
+                next_raw = blob.get("next_id", 1)
+                next_id = max(1, int(next_raw) if isinstance(next_raw, int | str) else 1)
+            except msgspec.ValidationError, TypeError, ValueError:
+                return cls()
+            groups = [TodoGroup(items=items)] if items else []
+            return cls(TodoStackData(groups=groups, next_id=next_id))
+
+        return cls()
+
+    def to_raw(self) -> dict[str, object]:
+        out: object = msgspec.to_builtins(self._data)
+        if not isinstance(out, dict):
+            return {"groups": [], "next_id": 1}
+        raw = cast("dict[object, object]", out)
+        return {str(key): value for key, value in raw.items()}
+
+    def render(self) -> str:
+        if not self._data.groups:
+            return "(todo stack empty — no groups)"
+        lines: list[str] = [
+            f"(LIFO of groups: depth={self.depth}; TOP group = current breakdown level)",
+        ]
+        # Top group first for the model.
+        for offset, group in enumerate(reversed(self._data.groups)):
+            depth = self.depth - 1 - offset
+            tag = " TOP" if offset == 0 else ""
+            lines.append(f"group d={depth}{tag}:")
+            if not group.items:
+                lines.append("  (empty group)")
+                continue
+            for item in group.items:
+                mark = {
+                    "pending": "[ ]",
+                    "in_progress": "[~]",
+                    "done": "[x]",
+                    "cancelled": "[-]",
+                }.get(item.status, "[?]")
+                note = f" — {item.notes}" if item.notes else ""
+                lines.append(f"  {mark} {item.id}: {item.title}{note}")
+        return "\n".join(lines)
+
+    def review_prompt(self) -> str:
+        """Compact, model-facing nag: open work still exists this turn."""
+        open_items = self.open_items()
+        n_open = len(open_items)
+        n_groups = self.depth
+        lines = [
+            f"[TODO OPEN] {n_open} open item(s) across {n_groups} group(s) "
+            f"(not empty). You did not call todo_* this turn.",
+            "Tools: todo_list | todo_push(titles=[...]) | todo_update | todo_pop | todo_clear",
+            "Rules: TOP group = current level; push=one sibling group; pop=remove whole TOP group.",
+            "Act on open work before ending (finish/pop TOP, or push child tasks). Stack:",
+            self.render(),
+        ]
+        return "\n".join(lines)
+
+    def _existing_numeric_ids(self) -> list[int]:
+        """Numeric suffixes of ids that look like ``tN`` (for counter reuse)."""
+        return [
+            int(item.id[1:])
+            for group in self._data.groups
+            for item in group.items
+            if item.id.startswith("t") and item.id[1:].isdigit()
+        ]
+
+    def _sync_next_id(self) -> None:
+        """Set ``next_id`` to one past the highest live id (or 1 if empty)."""
+        nums = self._existing_numeric_ids()
+        self._data.next_id = max(nums) + 1 if nums else 1
+
+    def _alloc(self, title: str, *, notes: str, status: TodoStatus) -> TodoItem:
+        item_id = f"t{self._data.next_id}"
+        self._data.next_id += 1
+        return TodoItem(id=item_id, title=title, status=status, notes=notes)
+
+    def push_group(
+        self,
+        titles: list[str],
+        *,
+        notes: str = "",
+        status: TodoStatus = "pending",
+    ) -> TodoGroup:
+        """Push **one** new group containing all *titles* as siblings."""
+        cleaned = [t.strip() for t in titles if t and t.strip()]
+        if not cleaned:
+            msg = "at least one non-empty title is required"
+            raise ValueError(msg)
+        note = notes.strip()
+        # Rebase counter on live ids so clear/pop do not leave a high watermark.
+        self._sync_next_id()
+        items = [self._alloc(title, notes=note, status=status) for title in cleaned]
+        group = TodoGroup(items=items)
+        self._data.groups.append(group)
+        self.mark_touched()
+        return group
+
+    def push(self, title: str, *, notes: str = "", status: TodoStatus = "pending") -> TodoItem:
+        """Push a group with a single task (still one stack level)."""
+        group = self.push_group([title], notes=notes, status=status)
+        return group.items[0]
+
+    def pop(self) -> TodoGroup | None:
+        """Pop and return the **top group** (all siblings in that push)."""
+        if not self._data.groups:
+            return None
+        group = self._data.groups.pop()
+        self._sync_next_id()
+        self.mark_touched()
+        return group
+
+    def clear(self) -> int:
+        n = sum(len(g.items) for g in self._data.groups)
+        self._data.groups.clear()
+        self._sync_next_id()
+        if n:
+            self.mark_touched()
+        return n
+
+    def get(self, item_id: str) -> TodoItem | None:
+        for item in self.all_items():
+            if item.id == item_id:
+                return item
+        return None
+
+    def update(
+        self,
+        item_id: str,
+        *,
+        title: str | None = None,
+        status: TodoStatus | None = None,
+        notes: str | None = None,
+    ) -> TodoItem:
+        for group in self._data.groups:
+            for index, item in enumerate(group.items):
+                if item.id != item_id:
+                    continue
+                new_title = title.strip() if title is not None else item.title
+                if not new_title:
+                    msg = "title must not be empty"
+                    raise ValueError(msg)
+                new_status = status if status is not None else item.status
+                new_notes = notes if notes is not None else item.notes
+                updated = TodoItem(id=item.id, title=new_title, status=new_status, notes=new_notes)
+                group.items[index] = updated
+                self.mark_touched()
+                return updated
+        msg = f"unknown todo id {item_id!r}"
+        raise KeyError(msg)
+
+
+def parse_push_titles(raw: str) -> list[str]:
+    """Parse multi-title push: JSON array, newlines, or ``;``-separated."""
+    text = raw.strip()
+    if not text:
+        return []
+    if text.startswith("["):
+        try:
+            data: object = msgspec.json.decode(text.encode())
+        except msgspec.DecodeError, UnicodeEncodeError:
+            data = None
+        if isinstance(data, list):
+            out = [item.strip() for item in cast("list[object]", data) if isinstance(item, str) and item.strip()]
+            if out:
+                return out
+    parts: list[str] = []
+    for line in text.replace(";", "\n").splitlines():
+        token = line.strip()
+        if token:
+            parts.append(token)
+    return parts

src/plyngent/agent/tools.py

@@ -13,9 +13,11 @@ from plyngent.typedef import JSONSchema  # noqa: TC001
 
 type ToolHandler = Callable[..., Any | Awaitable[Any]]
 type DangerClassifier = Callable[[str, Mapping[str, object]], str | None]
+# Returns True to allow, False to deny, or a non-empty str as denial reason for the model.
+type ToolConfirmResult = bool | str
 type ToolConfirmHook = Callable[
     [str, Mapping[str, object], str],
-    bool | Awaitable[bool],
+    ToolConfirmResult | Awaitable[ToolConfirmResult],
 ]
 
 _PRIMITIVE_SCHEMA: dict[type, JSONSchema] = {
@@ -212,7 +214,11 @@ class ToolRegistry:
         return msgspec.json.encode(result).decode()
 
     async def _maybe_confirm(self, name: str, args: dict[str, object]) -> str | None:
-        """Return an error string if the user denies a dangerous tool, else None."""
+        """If confirm is required and denied, return an error string for the model.
+
+        The confirm hook may return ``True`` (allow), ``False`` (deny), or a
+        non-empty string (deny with user comment for the model).
+        """
         if self._danger is None or self._on_confirm is None:
             return None
         reason = self._danger(name, args)
@@ -223,12 +229,14 @@ class ToolRegistry:
             reason = self._danger(name, args)
             if reason is None:
                 return None
-            allowed = self._on_confirm(name, args, reason)
-            if inspect.isawaitable(allowed):
-                allowed = await allowed
-            if allowed:
+            decision = self._on_confirm(name, args, reason)
+            if inspect.isawaitable(decision):
+                decision = await decision
+            if decision is True:
                 return None
-        return f"error: user denied tool {name!r} ({reason})"
+            if isinstance(decision, str) and decision.strip():
+                return f"error: tool {name!r} denied by user confirm ({reason}); user comment: {decision.strip()}"
+            return f"error: tool {name!r} denied by user confirm ({reason})"
 
     async def execute(self, name: str, arguments_json: str) -> str:
         """Run a tool by name; returns a string result (errors become error text)."""

src/plyngent/cli/app.py

@@ -257,7 +257,7 @@ async def _run_chat(  # noqa: C901, PLR0912, PLR0915 — chat orchestration
             try:
                 if client_supports_models(client):
                     remote_ids = await fetch_remote_model_ids(client)
-            except (RuntimeError, TypeError, OSError, ValueError):
+            except RuntimeError, TypeError, OSError, ValueError:
                 remote_ids = None
             choices = model_choices_for_provider(provider, remote_ids=remote_ids)
             model_id = select_model(
@@ -307,8 +307,10 @@ async def _run_chat(  # noqa: C901, PLR0912, PLR0915 — chat orchestration
     finally:
         await memory.close()
         from plyngent.tools.process.pty_session import PtyManager
+        from plyngent.tools.temp_workspace import cleanup_temporary_workspaces
 
         PtyManager.close_all()
+        _ = cleanup_temporary_workspaces()
 
 
 def _configure_logging(level: str) -> None:

src/plyngent/cli/interrupt.py

@@ -4,7 +4,6 @@ import asyncio
 import contextlib
 import signal
 from contextlib import contextmanager
-from contextvars import ContextVar
 from typing import TYPE_CHECKING
 
 if TYPE_CHECKING:
@@ -13,13 +12,16 @@ if TYPE_CHECKING:
 
     type SigHandler = Callable[[int, FrameType | None], None] | int | None
 
-_allow_task_cancel: ContextVar[bool] = ContextVar("allow_task_cancel", default=True)
+# Depth of nested pause_task_cancel_for_prompt. Must be a plain int (not ContextVar):
+# asyncio.add_signal_handler freezes the ContextVar snapshot at install time, so a
+# ContextVar reset after reinstall would leave SIGINT permanently non-cancelling.
+_prompt_depth: int = 0
 _reinstall_holder: list[Callable[[], None] | None] = [None]
 
 
 def allow_task_cancel() -> bool:
     """Whether the CLI SIGINT handler should cancel the in-flight turn task."""
-    return _allow_task_cancel.get()
+    return _prompt_depth == 0
 
 
 def set_sigint_reinstall(callback: Callable[[], None] | None) -> None:
@@ -34,8 +36,14 @@ def pause_task_cancel_for_prompt() -> Generator[None]:
     Must run on the main thread (signal handlers are main-thread only).
     Restores the default SIGINT handler so ``click.confirm`` can receive
     KeyboardInterrupt / Abort instead of the asyncio turn being cancelled.
+
+    Nested prompts are supported via a depth counter. The asyncio SIGINT
+    handler is reinstalled only after depth returns to 0, and only after
+    cancel is re-enabled, so the handler never freezes ``allow=False``.
     """
-    token = _allow_task_cancel.set(False)
+
+    global _prompt_depth  # noqa: PLW0603
+    _prompt_depth += 1
     loop_handler_removed = False
     previous: SigHandler = signal.SIG_DFL
     try:
@@ -56,11 +64,15 @@ def pause_task_cancel_for_prompt() -> Generator[None]:
     finally:
         with contextlib.suppress(ValueError):
             _ = signal.signal(signal.SIGINT, previous)
+        _prompt_depth = max(0, _prompt_depth - 1)
+        # Reinstall only when fully out of prompts and cancel is allowed again.
+        # Order matters: decrement depth first so allow_task_cancel() is True
+        # before reinstall (and handlers never freeze allow=False).
+        if _prompt_depth == 0 and loop_handler_removed:
             reinstall = _reinstall_holder[0]
-        if loop_handler_removed and reinstall is not None:
+            if reinstall is not None:
                 with contextlib.suppress(RuntimeError, NotImplementedError, ValueError):
                     reinstall()
-        _allow_task_cancel.reset(token)
 
 
 async def run_in_prompt_thread[**P, R](func: Callable[P, R], *args: P.args, **kwargs: P.kwargs) -> R:

src/plyngent/cli/limits.py

@@ -1,16 +1,20 @@
 from __future__ import annotations
 
+import shutil
 from typing import TYPE_CHECKING, Literal
 
 from plyngent.cli.interrupt import pause_task_cancel_for_prompt
 from plyngent.prompting import (
     ChoiceOption,
     NonInteractiveError,
+    ask,
+    ask_async,
     choose,
     choose_async,
     configure_prompting,
     confirm,
     confirm_async,
+    get_prompt_backend,
 )
 from plyngent.tools.process.pty_session import PtyManager
 
@@ -19,6 +23,78 @@ if TYPE_CHECKING:
 
 type WorkspaceMismatchChoice = Literal["keep", "rebind", "abort"]
 
+_BOX_MIN_WIDTH = 40
+_BOX_MAX_WIDTH = 100
+_BOX_PAD = 2  # spaces inside left/right borders
+
+
+def _terminal_width() -> int:
+    try:
+        return max(_BOX_MIN_WIDTH, min(_BOX_MAX_WIDTH, shutil.get_terminal_size(fallback=(80, 24)).columns))
+    except OSError:
+        return 80
+
+
+def _wrap_line(text: str, width: int) -> list[str]:
+    """Hard-wrap a single logical line to *width* (no word-break library)."""
+    width = max(width, 8)
+    if not text:
+        return [""]
+    if len(text) <= width:
+        return [text]
+    out: list[str] = []
+    rest = text
+    while rest:
+        if len(rest) <= width:
+            out.append(rest)
+            break
+        # Prefer break at last space in the window.
+        window = rest[:width]
+        break_at = window.rfind(" ")
+        if break_at >= width // 2:
+            out.append(rest[:break_at])
+            rest = rest[break_at + 1 :]
+        else:
+            out.append(rest[:width])
+            rest = rest[width:]
+    return out
+
+
+def format_tool_confirm_box(name: str, reason: str) -> str:
+    """Multi-line boxed confirm body (header + reason lines).
+
+    Printed with :meth:`PromptBackend.echo` before a short ``confirm()`` prompt
+    so terminals keep newlines (unlike a single jammed readline line).
+    """
+    term = _terminal_width()
+    inner = max(20, term - 4)  # room for ``│ `` + `` │``
+    header = f"confirm · tool {name!r}"
+    body_lines: list[str] = []
+    for raw in reason.replace("\r\n", "\n").replace("\r", "\n").split("\n"):
+        body_lines.extend(_wrap_line(raw, inner - _BOX_PAD))
+    content = [header, "─" * min(inner, max(len(header), 12)), *body_lines]
+    width = min(inner, max(len(line) for line in content) + _BOX_PAD)
+    width = max(width, min(inner, len(header) + _BOX_PAD))
+    top = "┌" + "─" * (width + 2) + "┐"
+    bottom = "└" + "─" * (width + 2) + "┘"
+    rows = [top]
+    for line in content:
+        # Second line is a separator drawn with box dashes already in content.
+        if line.startswith("─") and set(line) <= {"─"}:
+            rows.append("├" + "─" * (width + 2) + "┤")
+            continue
+        padded = line[:width].ljust(width)
+        rows.append(f"│ {padded} │")
+    rows.append(bottom)
+    return "\n".join(rows)
+
+
+def _echo_tool_confirm(name: str, reason: str) -> None:
+    backend = get_prompt_backend()
+    backend.echo()
+    backend.secho(format_tool_confirm_box(name, reason), fg="yellow")
+    backend.echo()
+
 
 def _prompt_continue_limit_sync(reason: str) -> bool:
     try:
@@ -44,33 +120,62 @@ async def prompt_continue_limit_async(reason: str) -> bool:
         return False
 
 
-def _prompt_confirm_tool_sync(name: str, args: Mapping[str, object], reason: str) -> bool:
+def _prompt_confirm_tool_sync(name: str, args: Mapping[str, object], reason: str) -> bool | str:
+    """True allow; False deny; non-empty str = deny with comment for the model."""
     del args
     try:
-        return confirm(
-            f"[confirm] tool {name!r}: {reason}\nAllow this tool call?",
-            default=False,
-        )
+        _echo_tool_confirm(name, reason)
+        allowed = confirm("Allow this tool call?", default=False)
     except NonInteractiveError:
         return False
+    if allowed:
+        return True
+    try:
+        comment = ask(
+            "Optional comment for the agent (why denied; empty to skip):",
+            default="",
+        ).strip()
+    except NonInteractiveError:
+        return False
+    return comment or False
 
 
-def prompt_confirm_tool(name: str, args: Mapping[str, object], reason: str) -> bool:
-    """Ask whether to allow a destructive tool call (TTY). Default is deny."""
+def prompt_confirm_tool(name: str, args: Mapping[str, object], reason: str) -> bool | str:
+    """Ask whether to allow a dangerous tool call (TTY). Default is deny.
+
+    Prints a multi-line boxed summary, then a short y/N prompt. On deny,
+    optionally collect a free-text comment for the model.
+    """
     with pause_task_cancel_for_prompt():
         return _prompt_confirm_tool_sync(name, args, reason)
 
 
-async def prompt_confirm_tool_async(name: str, args: Mapping[str, object], reason: str) -> bool:
-    """Async variant: confirm off the event loop."""
+async def prompt_confirm_tool_async(name: str, args: Mapping[str, object], reason: str) -> bool | str:
+    """Async confirm: True allow, False deny, str = deny with user comment."""
     del args
     try:
-        return await confirm_async(
-            f"[confirm] tool {name!r}: {reason}\nAllow this tool call?",
-            default=False,
-        )
+        # Box is printed inside the worker thread via confirm's backend.
+        def _run() -> bool:
+            _echo_tool_confirm(name, reason)
+            return confirm("Allow this tool call?", default=False)
+
+        from plyngent.prompting import run_prompt_async
+
+        allowed = await run_prompt_async(_run)
     except NonInteractiveError:
         return False
+    if allowed:
+        return True
+    try:
+        comment = (
+            await ask_async(
+                "Optional comment for the agent (why denied; empty to skip):",
+                default="",
+            )
+        ).strip()
+    except NonInteractiveError:
+        return False
+    return comment or False
 
 
 def _prompt_workspace_mismatch_sync(

src/plyngent/cli/readline_setup.py

@@ -54,8 +54,10 @@ def build_completer(state: ReplState) -> Callable[[str, int], str | None]:
             options = filter_prefix(text, slash_commands())
         else:
             head = buffer[:begidx].strip()
-            command = head.split()[0] if head else ""
-            options = complete_slash_args(state, command, text)
+            tokens = head.split() if head else []
+            command = tokens[0] if tokens else ""
+            prior_args = tokens[1:] if len(tokens) > 1 else []
+            options = complete_slash_args(state, command, text, prior_args=prior_args)
         if state_index < len(options):
             return options[state_index]
         return None

src/plyngent/cli/retry.py

@@ -66,6 +66,9 @@ async def run_cancellable[T](coro: Coroutine[object, object, T]) -> T:
     installed = False
 
     def _on_sigint() -> None:
+        # allow_task_cancel() uses a process-level depth counter (not ContextVar)
+        # so this remains correct even if the handler was installed under a
+        # frozen context (asyncio signal handles capture contextvars).
         if allow_task_cancel() and not task.done():
             _ = task.cancel()
 

src/plyngent/cli/slash.py

@@ -15,7 +15,8 @@ from plyngent.cli.selection import select_model, select_provider
 from plyngent.lmproto.openai_compatible.model import (
     AssistantChatMessage,
     AssistantFunctionToolCall,
-    ToolChatMessage,
+    DeveloperChatMessage,
+    SystemChatMessage,
     UserChatMessage,
 )
 from plyngent.runtime import ProviderNotSupportedError
@@ -32,15 +33,58 @@ _COMPACT_PREVIEW = 400
 _ON_OFF_CHOICES = ("on", "off")
 _YOLO_MODE_CHOICES = ("on", "off", "once")
 _EXPORT_FORMAT_CHOICES = ("md", "json")
+_TODO_ACTION_CHOICES = (
+    "list",
+    "show",
+    "ls",
+    "push",
+    "pop",
+    "done",
+    "cancel",
+    "pending",
+    "in_progress",
+    "clear",
+)
+_ROUNDS_CHOICES = ("8", "16", "32", "64", "128")
+
+
+class HistoryLimitType(click.ParamType[int]):
+    """``N`` (int >= 1) or the shortcut ``last`` (equivalent to ``1``)."""
+
+    name: str = "history_limit"
+
+    @override
+    def convert(self, value: object, param: click.Parameter | None, ctx: click.Context | None) -> int:
+        if isinstance(value, int):
+            if value < 1:
+                self.fail("must be >= 1", param, ctx)
+            return value
+        text = str(value).strip().lower()
+        if text == "last":
+            return 1
+        try:
+            n = int(text, 10)
+        except ValueError:
+            self.fail("expected an integer N or 'last'", param, ctx)
+        if n < 1:
+            self.fail("must be >= 1", param, ctx)
+        return n
+
+    @override
+    def shell_complete(self, ctx: click.Context, param: click.Parameter, incomplete: str) -> list[CompletionItem]:
+        del ctx, param
+        tokens = ("last", "1", "5", "10", "20")
+        return [CompletionItem(token) for token in tokens if incomplete == "" or token.startswith(incomplete.lower())]
+
 
 HELP_FOOTER = (
     "User messages are saved immediately. On API errors or Ctrl+C, partial\n"
     "assistant/tool output is discarded but the user message stays (so /retry\n"
     "works after resume, not only via readline history). Auto-retry: 10s/20s/30s.\n"
     "\n"
-    "Tab completes slash commands and some arguments (provider, model, tools,\n"
-    "stream, verbose, yolo, export). Use --session ID or /resume to continue a prior\n"
-    "chat after restart.\n"
+    "Tab completes slash commands and arguments (provider, model, session ids,\n"
+    "todos actions, on/off, yolo, export, flags). Use --session ID or /resume to\n"
+    "continue a prior chat after restart.\n"
     "\n"
     'Multiline: start a message with """ then end a later line with """.\n'
     "Long prompts: /edit opens $EDITOR.\n"
@@ -130,6 +174,80 @@ class ExportFormatParam(click.ParamType[str]):
 EXPORT_FORMAT = ExportFormatParam()
 
 
+class TodosActionParam(click.ParamType[str]):
+    """First token of ``/todos``: list|push|pop|done|…"""
+
+    name: str = "todos_action"
+
+    @override
+    def convert(self, value: Any, param: click.Parameter | None, ctx: click.Context | None) -> str:
+        del param, ctx
+        return str(value)
+
+    @override
+    def shell_complete(self, ctx: click.Context, param: click.Parameter, incomplete: str) -> list[CompletionItem]:
+        del ctx, param
+        return _filter_choices(incomplete, _TODO_ACTION_CHOICES)
+
+
+TODOS_ACTION = TodosActionParam()
+
+
+class SessionIdParam(click.ParamType[int]):
+    """Session id for ``/resume`` / ``/delete`` (from ReplState cache + current)."""
+
+    name: str = "session_id"
+
+    @override
+    def convert(self, value: Any, param: click.Parameter | None, ctx: click.Context | None) -> int:
+        if isinstance(value, int):
+            return value
+        text = str(value).strip()
+        try:
+            return int(text, 10)
+        except ValueError:
+            self.fail("expected a session id (integer)", param, ctx)
+
+    @override
+    def shell_complete(self, ctx: click.Context, param: click.Parameter, incomplete: str) -> list[CompletionItem]:
+        del param
+        state = _repl_state(ctx)
+        if state is None:
+            return []
+        # Sync cache only — no async from readline Tab (no awaitlet greenlet).
+        return _filter_choices(incomplete, state.session_ids_for_complete())
+
+
+SESSION_ID = SessionIdParam()
+
+
+class RoundsParam(click.ParamType[int]):
+    """Max tool-loop rounds (int >= 1); Tab suggests common values."""
+
+    name: str = "rounds"
+
+    @override
+    def convert(self, value: Any, param: click.Parameter | None, ctx: click.Context | None) -> int:
+        if isinstance(value, int):
+            n = value
+        else:
+            try:
+                n = int(str(value).strip(), 10)
+            except ValueError:
+                self.fail("expected an integer >= 1", param, ctx)
+        if n < 1:
+            self.fail("max_rounds must be >= 1", param, ctx)
+        return n
+
+    @override
+    def shell_complete(self, ctx: click.Context, param: click.Parameter, incomplete: str) -> list[CompletionItem]:
+        del ctx, param
+        return _filter_choices(incomplete, _ROUNDS_CHOICES)
+
+
+ROUNDS = RoundsParam()
+
+
 class ProviderNameParam(click.ParamType[str]):
     name: str = "provider"
 
@@ -232,21 +350,55 @@ def slash_command_names() -> list[str]:
     return sorted(f"/{name}" for name in slash.list_commands(ctx))
 
 
-def complete_slash_args(state: ReplState, command: str, incomplete: str) -> list[str]:
-    """Tab-complete arguments for ``command`` (e.g. ``/stream``) from ParamTypes.
+def complete_slash_args(
+    state: ReplState,
+    command: str,
+    incomplete: str,
+    *,
+    prior_args: Sequence[str] | None = None,
+) -> list[str]:
+    """Tab-complete arguments/options for ``command`` from ParamTypes.
 
-    Uses the first :class:`click.Argument` on the registered command whose type
-    implements :meth:`~click.ParamType.shell_complete` with candidates.
+    *prior_args* are tokens already typed after the command name (so
+    ``/todos done t`` can complete todo ids). Options are completed when
+    *incomplete* starts with ``-``.
     """
     name = command.lstrip("/").lower()
     ctx = click.Context(slash, obj=state)
     cmd = slash.get_command(ctx, name)
     if cmd is None:
         return []
+    prior = list(prior_args or ())
+
     with click.Context(cmd, info_name=name, parent=ctx, obj=state) as sub:
-        for param in cmd.params:
-            if not isinstance(param, click.Argument):
-                continue
+        # Flag / option completion (e.g. --persist, --full).
+        if incomplete.startswith("-"):
+            flags = [
+                opt
+                for param in cmd.params
+                if isinstance(param, click.Option)
+                for opt in param.opts
+                if opt.startswith(incomplete)
+            ]
+            if flags:
+                return sorted(set(flags))
+
+        # Contextual /todos second token: todo ids after done|cancel|pending|in_progress.
+        if name == "todos" and prior:
+            action = prior[0].lower()
+            if action in {"done", "cancel", "pending", "in_progress"} and len(prior) == 1:
+                ids = [item.id for item in state.todo_stack.all_items()]
+                return [i for i in ids if i.startswith(incomplete)]
+
+        # Positional arguments: complete the next unset argument.
+        arg_params = [p for p in cmd.params if isinstance(p, click.Argument)]
+        arg_index = len(prior)
+        if arg_index < len(arg_params):
+            param = arg_params[arg_index]
+            items = param.type.shell_complete(sub, param, incomplete)
+            if items:
+                return [item.value for item in items]
+        for param in arg_params:
             items = param.type.shell_complete(sub, param, incomplete)
             if items:
                 return [item.value for item in items]
@@ -398,6 +550,7 @@ def status_cmd(state: ReplState) -> None:
 def sessions_cmd(state: ReplState) -> None:
     """List sessions for this workspace (newest first)."""
     sessions = _await(state.memory.list_sessions(workspace=state.workspace))
+    state.remember_session_ids([s.sid for s in sessions])
     if not sessions:
         click.echo(f"(no sessions for workspace {state.workspace})")
         return
@@ -435,7 +588,7 @@ def rename_cmd(state: ReplState, name: tuple[str, ...]) -> None:
 
 
 @slash.command("delete")
-@click.argument("session_id", type=int, required=False)
+@click.argument("session_id", type=SESSION_ID, required=False)
 @click.pass_obj
 def delete_cmd(state: ReplState, session_id: int | None) -> None:
     """Hard-delete a session (confirm; current → new empty)."""
@@ -538,7 +691,7 @@ def export_cmd(state: ReplState, parts: tuple[str, ...]) -> None:
 
 
 @slash.command("resume")
-@click.argument("session_id", type=int, required=False)
+@click.argument("session_id", type=SESSION_ID, required=False)
 @click.pass_obj
 def resume_cmd(state: ReplState, session_id: int | None) -> None:
     """Resume session id, or latest for this workspace if omitted."""
@@ -576,6 +729,11 @@ def compact_cmd(state: ReplState, name: str | None) -> None:
         return
     preview = summary if len(summary) <= _COMPACT_PREVIEW else summary[:_COMPACT_PREVIEW] + "…"
     click.echo(f"compacted session {old_id} -> new session {new_id}")
+    click.secho(
+        f"active session is summary-only ({len(state.agent.messages)} messages); "
+        f"full history remains on /resume {old_id}",
+        fg="bright_black",
+    )
     click.secho(preview, fg="bright_black")
 
 
@@ -637,8 +795,13 @@ def provider_cmd(state: ReplState, name: str | None) -> None:
 
 @slash.command("models")
 @click.option("--refresh", is_flag=True, help="Bypass cache and re-fetch GET /models.")
+@click.option(
+    "--persist",
+    is_flag=True,
+    help="Merge remote (and recovered) model ids into plyngent.toml for this provider.",
+)
 @click.pass_obj
-def models_cmd(state: ReplState, *, refresh: bool) -> None:
+def models_cmd(state: ReplState, *, refresh: bool, persist: bool) -> None:  # noqa: C901
     """List models (remote-first, plus config-only ids). Always tries GET /models."""
     del refresh  # always re-fetch; flag kept for CLI compatibility / docs
     remote: list[str] | None = None
@@ -662,6 +825,14 @@ def models_cmd(state: ReplState, *, refresh: bool) -> None:
         except (KeyError, ValueError) as exc:
             click.secho(f"could not recover provider: {exc}", fg="yellow", err=True)
 
+    if persist:
+        try:
+            path = state.persist_models_to_config(mode="catalog", catalog_ids=remote or ())
+            click.echo(f"persisted {len(state.provider.models)} model(s) for {state.provider_name!r} to {path}")
+        except (KeyError, ValueError, OSError) as exc:
+            click.secho(f"error: could not persist models: {exc}", fg="red")
+            return
+
     config_ids = set(state.config_model_ids())
     choices = model_choices_for_provider(state.provider, remote_ids=remote)
 
@@ -691,12 +862,20 @@ def models_cmd(state: ReplState, *, refresh: bool) -> None:
 
 @slash.command("model")
 @click.argument("model_id", required=False, type=MODEL_ID)
+@click.option(
+    "--persist",
+    is_flag=True,
+    help="Write the current (or newly selected) model id into plyngent.toml.",
+)
 @click.pass_obj
-def model_cmd(state: ReplState, model_id: str | None) -> None:
-    """Show or switch model (Tab: remote-first plus config; live fetch on pick)."""
-    if not model_id:
-        click.echo(f"model={state.model}")
-        return
+def model_cmd(state: ReplState, model_id: str | None, *, persist: bool) -> None:
+    """Show or switch model (Tab: remote-first plus config; live fetch on pick).
+
+    ``/model --persist`` saves the active model id into the provider catalog in
+    TOML (faster Tab/list on next launch). ``/model <id> --persist`` switches
+    then saves.
+    """
+    if model_id:
         try:
             choices = _await(state.merged_model_choices(refresh=True))
             state.model = select_model(
@@ -709,6 +888,17 @@ def model_cmd(state: ReplState, model_id: str | None) -> None:
             click.echo(f"switched model to {state.model}")
         except click.ClickException as exc:
             click.echo(f"error: {exc}")
+            return
+    elif not persist:
+        click.echo(f"model={state.model}")
+        return
+
+    if persist:
+        try:
+            path = state.persist_models_to_config(mode="current")
+            click.echo(f"persisted model {state.model!r} for {state.provider_name!r} to {path}")
+        except (KeyError, ValueError, OSError) as exc:
+            click.secho(f"error: could not persist model: {exc}", fg="red")
 
 
 @slash.command("tools")
@@ -800,45 +990,160 @@ def markdown_cmd(state: ReplState, enabled: bool | None) -> None:  # noqa: FBT00
 
 
 @slash.command("rounds")
-@click.argument("n", required=False, type=int)
+@click.argument("n", required=False, type=ROUNDS)
 @click.pass_obj
 def rounds_cmd(state: ReplState, n: int | None) -> None:
     """Show or set max tool-loop rounds."""
     if n is None:
         click.echo(f"max_rounds={state.max_rounds}")
         return
-    if n < 1:
-        msg = "max_rounds must be >= 1"
-        raise click.UsageError(msg)
     state.max_rounds = n
     state.agent.max_rounds = n
     click.echo(f"max_rounds={state.max_rounds}")
 
 
 @slash.command("history")
-@click.argument("n", required=False, type=int)
+@click.argument("n", required=False, type=HistoryLimitType())
+@click.option(
+    "--full",
+    "mode_full",
+    is_flag=True,
+    default=False,
+    help="Print full message bodies (markdown for assistant when TTY).",
+)
+@click.option(
+    "--preview",
+    "mode_preview",
+    is_flag=True,
+    default=False,
+    help="Force short previews even for a single message.",
+)
 @click.pass_obj
-def history_cmd(state: ReplState, n: int | None) -> None:
-    """Show last n messages in this session (default 20)."""
-    limit = _DEFAULT_HISTORY_LINES if n is None else n
-    if limit < 1:
-        msg = "n must be >= 1"
+def history_cmd(
+    state: ReplState,
+    n: int | None,
+    *,
+    mode_full: bool,
+    mode_preview: bool,
+) -> None:
+    """Show recent messages (default: last 20 as short previews).
+
+    ``/history last`` or ``/history 1`` shows the last message in full with Rich
+    markdown when available. Use ``--full`` for multiple messages in full;
+    ``--preview`` forces the short form even for a single message.
+    """
+    if mode_full and mode_preview:
+        msg = "use only one of --full / --preview"
         raise click.UsageError(msg)
+    limit = _DEFAULT_HISTORY_LINES if n is None else n
     messages = state.agent.messages
     if not messages:
         click.echo("(no messages in this session)")
         return
     start = max(0, len(messages) - limit)
-    click.echo(f"session={state.session_id}  messages={len(messages)}  showing={len(messages) - start}")
-    for offset, message in enumerate(messages[start:]):
-        click.echo(_format_history_message(start + offset, message))
+    slice_msgs = messages[start:]
+    # Full: --full, or single-message window (last / 1) unless --preview.
+    full = mode_full or (len(slice_msgs) == 1 and not mode_preview)
+    mode_tag = "full" if full else "preview"
+    click.echo(f"session={state.session_id}  messages={len(messages)}  showing={len(slice_msgs)}  mode={mode_tag}")
+    for offset, message in enumerate(slice_msgs):
+        idx = start + offset
+        if full:
+            _print_history_message_full(idx, message)
+        else:
+            click.echo(_format_history_message(idx, message))
     if state.agent.pending_retry_text is not None:
+        pending = state.agent.pending_retry_text
+        if full:
+            click.secho("(pending retry) user:", fg="yellow")
+            click.echo(pending)
+        else:
             click.secho(
-            f"(pending retry) user: {_preview_content(state.agent.pending_retry_text)}",
+                f"(pending retry) user: {_preview_content(pending)}",
                 fg="yellow",
             )
 
 
+@slash.command("todos")
+@click.argument("action", required=False, type=TODOS_ACTION)
+@click.argument("rest", required=False, nargs=-1, type=str)
+@click.pass_obj
+def todos_cmd(  # noqa: C901, PLR0911, PLR0912, PLR0915
+    state: ReplState, action: str | None, rest: tuple[str, ...]
+) -> None:
+    """Show or edit the LIFO stack of **task groups**.
+
+    ``/todos`` — list (top group first)
+    ``/todos push T1; T2`` — one new group of siblings
+    ``/todos pop`` — pop entire top group
+    ``/todos done <id>`` / ``/todos cancel <id>`` — set status
+    ``/todos clear`` — wipe stack
+    """
+    from plyngent.agent.todo_stack import parse_push_titles
+
+    stack = state.todo_stack
+    act = (action or "list").strip().lower()
+    if act in {"list", "show", "ls"}:
+        click.echo(stack.render())
+        return
+    if act == "push":
+        raw = " ".join(rest).strip()
+        if not raw:
+            click.echo('error: usage: /todos push <title> | /todos push ["T1","T2"] | T1; T2')
+            return
+        titles = parse_push_titles(raw)
+        if not titles:
+            click.echo("error: no titles to push (use a JSON array or ; / newlines)")
+            return
+        try:
+            group = stack.push_group(titles)
+        except ValueError as exc:
+            click.echo(f"error: {exc}")
+            return
+        _await(state.persist_todo_stack())
+        ids = ", ".join(i.id for i in group.items)
+        click.echo(f"pushed group depth={stack.depth} items=[{ids}]")
+        click.echo(stack.render())
+        return
+    if act == "pop":
+        group = stack.pop()
+        if group is None:
+            click.echo("todo stack empty")
+            return
+        _await(state.persist_todo_stack())
+        titles = ", ".join(f"{i.id}:{i.title}" for i in group.items) or "(empty)"
+        click.echo(f"popped TOP group ({titles})")
+        click.echo(stack.render())
+        return
+    if act in {"done", "cancel", "pending", "in_progress"}:
+        if not rest:
+            click.echo(f"error: usage: /todos {act} <id>")
+            return
+        if act == "done":
+            new_status = "done"
+        elif act == "cancel":
+            new_status = "cancelled"
+        elif act == "pending":
+            new_status = "pending"
+        else:
+            new_status = "in_progress"
+        try:
+            item = stack.update(rest[0], status=new_status)
+        except (KeyError, ValueError) as exc:
+            click.echo(f"error: {exc}")
+            return
+        _await(state.persist_todo_stack())
+        click.echo(f"updated {item.id} → {item.status}")
+        click.echo(stack.render())
+        return
+    if act == "clear":
+        n = stack.clear()
+        _await(state.persist_todo_stack())
+        click.echo(f"cleared {n} item(s)")
+        return
+    click.echo("error: usage: /todos [list|push|pop|done|cancel|clear] …")
+
+
 @slash.command("retry")
 @click.pass_obj
 def retry_cmd(state: ReplState) -> None:
@@ -858,9 +1163,71 @@ def _preview_content(text: str | None) -> str:
     return text[:_CONTENT_PREVIEW] + "…"
 
 
+def _print_history_assistant_full(index: int, message: AssistantChatMessage) -> None:
+    from plyngent.cli.display import markdown_render_available, print_markdown
+
+    click.secho(f"{index}. assistant:", fg="cyan")
+    content = message.content
+    has_text = isinstance(content, str) and content.strip()
+    if has_text and isinstance(content, str):
+        if markdown_render_available():
+            print_markdown(content, label="")
+        else:
+            click.echo(content)
+    reasoning = message.reasoning_content
+    has_reason = isinstance(reasoning, str) and reasoning.strip()
+    if has_reason and isinstance(reasoning, str):
+        click.secho("reasoning:", fg="bright_black")
+        click.echo(reasoning)
+    tool_calls = message.tool_calls
+    has_tools = tool_calls is not UNSET and bool(tool_calls)
+    if has_tools and tool_calls is not UNSET:
+        for call in tool_calls:
+            if isinstance(call, AssistantFunctionToolCall):
+                click.secho(
+                    f"  tool_call {call.id}: {call.function.name}({call.function.arguments})",
+                    fg="yellow",
+                )
+            else:
+                click.secho(f"  tool_call custom id={call.id}", fg="yellow")
+    if not (has_text or has_reason or has_tools):
+        click.echo("(empty)")
+    click.echo()
+
+
+def _print_history_message_full(index: int, message: AnyChatMessage) -> None:
+    """Print one history message with full body; Rich markdown for assistant text."""
+    if isinstance(message, UserChatMessage):
+        click.secho(f"{index}. user:", fg="green")
+        click.echo(message.content or "")
+        click.echo()
+        return
+    if isinstance(message, DeveloperChatMessage):
+        click.secho(f"{index}. developer:", fg="blue")
+        click.echo(message.content or "")
+        click.echo()
+        return
+    if isinstance(message, SystemChatMessage):
+        click.secho(f"{index}. system:", fg="bright_black")
+        click.echo(message.content or "")
+        click.echo()
+        return
+    if isinstance(message, AssistantChatMessage):
+        _print_history_assistant_full(index, message)
+        return
+    # ToolChatMessage (remaining AnyChatMessage arm)
+    click.secho(f"{index}. tool({message.tool_call_id}):", fg="magenta")
+    click.echo(message.content or "")
+    click.echo()
+
+
 def _format_history_message(index: int, message: AnyChatMessage) -> str:
     if isinstance(message, UserChatMessage):
         return f"{index}. user: {_preview_content(message.content)}"
+    if isinstance(message, DeveloperChatMessage):
+        return f"{index}. developer: {_preview_content(message.content)}"
+    if isinstance(message, SystemChatMessage):
+        return f"{index}. system: {_preview_content(message.content)}"
     if isinstance(message, AssistantChatMessage):
         parts: list[str] = []
         if isinstance(message.content, str) and message.content:
@@ -876,11 +1243,8 @@ def _format_history_message(index: int, message: AnyChatMessage) -> str:
             parts.append(f"tool_calls=[{', '.join(names)}]")
         body = " ".join(parts) if parts else "(empty)"
         return f"{index}. assistant: {body}"
-    if isinstance(message, ToolChatMessage):
+    # ToolChatMessage
     return f"{index}. tool({message.tool_call_id}): {_preview_content(message.content)}"
-    role = getattr(message, "role", type(message).__name__)
-    content = getattr(message, "content", "")
-    return f"{index}. {role}: {_preview_content(str(content))}"
 
 
 def _run_slash_argv(args: Sequence[str], state: ReplState) -> None:

src/plyngent/cli/state.py

@@ -8,6 +8,7 @@ from typing import TYPE_CHECKING, Literal, cast
 
 from plyngent.agent import ChatAgent, ChatClient, ToolRegistry
 from plyngent.agent.loop import DEFAULT_MAX_ROUNDS
+from plyngent.agent.todo_stack import TodoStack
 from plyngent.cli.models_source import (
     DEFAULT_MODELS_CACHE_TTL,
     client_supports_models,
@@ -17,9 +18,11 @@ from plyngent.cli.models_source import (
 )
 from plyngent.memory.database.store import normalize_workspace
 from plyngent.runtime import create_client
-from plyngent.tools import DEFAULT_TOOLS, set_workspace_root
+from plyngent.tools import DEFAULT_TOOLS, set_todo_stack, set_workspace_root
 
 if TYPE_CHECKING:
+    from collections.abc import Sequence
+
     from plyngent.config.models import Provider
     from plyngent.config.store import ConfigStore
     from plyngent.memory import MemoryStore
@@ -54,6 +57,10 @@ class ReplState:
     client: ChatClient = field(init=False)
     agent: ChatAgent = field(init=False)
     session_id: int | None = None
+    todo_stack: TodoStack = field(default_factory=TodoStack)
+    _todo_persist_tasks: set[object] = field(default_factory=set, init=False, repr=False)
+    # Session ids for Tab complete (updated when listing/creating/resuming).
+    _session_id_cache: list[int] = field(default_factory=list, init=False, repr=False)
     # Remote GET /models cache (per provider base).
     _remote_models: list[str] | None = field(default=None, init=False, repr=False)
     _remote_models_fetched_at: float | None = field(default=None, init=False, repr=False)
@@ -66,6 +73,7 @@ class ReplState:
         self.workspace = Path(self.workspace).expanduser().resolve()
         self.agent = self._make_agent()
         self.sync_display_flags()
+        self._bind_todo_tools()
 
     def sync_display_flags(self) -> None:
         from plyngent.cli.display import set_markdown_enabled, set_verbose_tool_results
@@ -107,6 +115,44 @@ class ReplState:
 
             click.secho("yolo=off (once expired)", fg="bright_black", err=True)
 
+    def _bind_todo_tools(self) -> None:
+        """Point module-level todo tools at this session stack + persist hook."""
+        import asyncio
+
+        def on_change() -> None:
+            if self.session_id is None:
+                return
+            try:
+                loop = asyncio.get_running_loop()
+            except RuntimeError:
+                return
+            task = loop.create_task(self.memory.update_session_todo_stack(self.session_id, self.todo_stack.to_raw()))
+            # Keep a strong ref until done so the task is not GC'd mid-flight.
+            self._todo_persist_tasks.add(task)
+            task.add_done_callback(self._todo_persist_tasks.discard)
+
+        set_todo_stack(self.todo_stack, on_change=on_change)
+
+    async def persist_todo_stack(self) -> None:
+        """Write the in-memory todo stack to the active session row."""
+        if self.session_id is None:
+            return
+        _ = await self.memory.update_session_todo_stack(self.session_id, self.todo_stack.to_raw())
+
+    async def load_todo_stack(self) -> None:
+        """Load todo stack from the active session (empty if none)."""
+        if self.session_id is None:
+            self.todo_stack = TodoStack()
+            self._bind_todo_tools()
+            if hasattr(self, "agent"):
+                self.agent.todo_stack = self.todo_stack
+            return
+        raw = await self.memory.get_session_todo_stack(self.session_id)
+        self.todo_stack = TodoStack.from_raw(raw)
+        self._bind_todo_tools()
+        if hasattr(self, "agent"):
+            self.agent.todo_stack = self.todo_stack
+
     def _tool_registry(self) -> ToolRegistry | None:
         if not self.tools_enabled:
             return None
@@ -140,18 +186,22 @@ class ReplState:
             max_tool_result_chars=agent_cfg.max_tool_result_chars,
             parallel_tools=agent_cfg.parallel_tools,
             max_context_tokens=agent_cfg.max_context_tokens,
+            todo_stack=self.todo_stack,
         )
 
     def rebuild_client(self) -> None:
         """Recreate client and agent after provider/model/tools change."""
         messages = list(self.agent.messages)
+        persist_from = self.agent.persist_from
         # Preserve live stream toggle if agent already exists.
         if hasattr(self, "agent"):
             self.stream_enabled = self.agent.stream
         self.client = cast("ChatClient", cast("object", create_client(self.provider)))
         self.agent = self._make_agent()
-        self.agent.messages = messages
+        # Restore history without re-marking already-stored messages as dirty.
+        self.agent.replace_messages(messages, persist_from=persist_from)
         self.sync_display_flags()
+        self._bind_todo_tools()
         # Drop remote catalog when provider identity/url changed (not on model-only switch).
         if self._remote_models_key is not None and self._remote_models_key != self._models_cache_key():
             self.invalidate_remote_models()
@@ -174,6 +224,22 @@ class ReplState:
         self._remote_models_key = self._models_cache_key()
         self._remote_models_error = None
 
+    def remember_session_ids(self, ids: Sequence[int]) -> None:
+        """Cache session ids for Tab completion (``/resume`` / ``/delete``)."""
+        self._session_id_cache = [int(i) for i in ids]
+
+    def session_ids_for_complete(self) -> list[str]:
+        """String session ids for completers (cache + current session if any)."""
+        seen: set[int] = set()
+        out: list[str] = []
+        for sid in self._session_id_cache:
+            if sid not in seen:
+                seen.add(sid)
+                out.append(str(sid))
+        if self.session_id is not None and self.session_id not in seen:
+            out.insert(0, str(self.session_id))
+        return out
+
     def cached_remote_models(self) -> list[str] | None:
         """Return cached remote ids if still valid for the current provider."""
         if self._remote_models is None or self._remote_models_fetched_at is None:
@@ -290,6 +356,28 @@ class ReplState:
             model=self.model,
         )
 
+    def persist_models_to_config(
+        self,
+        *,
+        mode: Literal["current", "catalog"],
+        catalog_ids: Sequence[str] | None = None,
+    ) -> Path:
+        """Merge model id(s) into TOML for the current provider and write disk.
+
+        *mode* ``current``: ensure :attr:`model` is in the provider catalog.
+        *mode* ``catalog``: union *catalog_ids* (or empty) into the catalog.
+
+        Returns the config path written. Raises ``OSError`` / ``ValueError`` /
+        ``KeyError`` on failure.
+        """
+        if mode == "current":
+            self.provider = self.config.ensure_model(self.provider_name, self.model)
+        else:
+            ids = list(catalog_ids) if catalog_ids is not None else []
+            self.provider = self.config.merge_models(self.provider_name, ids)
+        self.config.write()
+        return self.config.path
+
     def _try_set_provider(self, pname: str) -> bool:
         import click
 
@@ -353,7 +441,11 @@ class ReplState:
             model=self.model,
         )
         self.session_id = session.sid
+        if session.sid not in self._session_id_cache:
+            self._session_id_cache.insert(0, session.sid)
+        self.todo_stack = TodoStack()
         self.agent = self._make_agent()
+        self._bind_todo_tools()
 
     async def rename_current_session(self, name: str) -> SessionRow:
         if self.session_id is None:
@@ -404,11 +496,14 @@ class ReplState:
                     raise ValueError(msg) from exc
 
         self.session_id = session_id
+        if session_id not in self._session_id_cache:
+            self._session_id_cache.insert(0, session_id)
         if self.apply_session_llm(row):
             self.rebuild_client()
         else:
             self.agent = self._make_agent()
         await self.agent.load_history()
+        await self.load_todo_stack()
 
     async def resume_latest_or_new(self, name: str = "chat") -> str:
         """Resume most recently updated session for this workspace, or create one."""
@@ -423,6 +518,7 @@ class ReplState:
         else:
             self.agent = self._make_agent()
         await self.agent.load_history()
+        await self.load_todo_stack()
         _ = await self.memory.touch_session(latest.sid)
         return "resume"
 
@@ -430,6 +526,7 @@ class ReplState:
         """Soft-compact + model-summarize current history into a new workspace session.
 
         Returns ``(old_session_id, new_session_id, summary)``.
+        Todo stack is carried into the new session.
         """
         from plyngent.agent.compact import build_compacted_seed_messages, summarize_messages
 
@@ -461,6 +558,7 @@ class ReplState:
             system_prompt=self.config.agent_config.compact_system_prompt or None,
             user_prefix=self.config.agent_config.compact_user_prefix or None,
         )
+        carried_todos = self.todo_stack.to_raw()
         session_name = name or f"compact-from-{old_id}"
         await self.new_session(name=session_name)
         new_id = self.session_id
@@ -474,7 +572,17 @@ class ReplState:
             source_session_id=old_id,
             seed_text=self.config.agent_config.compact_seed_text or None,
         )
-        self.agent.messages = list(seed)
         for message in seed:
             _ = await self.memory.append_message(new_id, message)
+        # Reload from DB so RAM matches stored rows and the persist cursor is correct
+        # (assigning messages alone left _persist_from at 0 and broke later checkpoints).
+        await self.agent.load_history()
+        if not self.agent.messages:
+            msg = f"compact session {new_id} has no messages after seed"
+            raise RuntimeError(msg)
+        # Carry open/closed todos so multi-step work survives compact.
+        self.todo_stack = TodoStack.from_raw(carried_todos)
+        self._bind_todo_tools()
+        self.agent.todo_stack = self.todo_stack
+        await self.persist_todo_stack()
         return old_id, new_id, summary

src/plyngent/config/store.py

@@ -200,6 +200,59 @@ class ConfigStore:
         _ = self._bad_providers.pop(name, None)
         return promoted
 
+    def _take_provider(self, name: str) -> Provider:
+        """Return a ready or recoverable provider, promoting recoverable into ready map."""
+        if name in self._providers:
+            return self._providers[name]
+        if name in self._recoverable_providers:
+            provider = self._recoverable_providers.pop(name)
+            self._providers[name] = provider
+            _ = self._bad_providers.pop(name, None)
+            return provider
+        msg = f"unknown provider {name!r}"
+        raise KeyError(msg)
+
+    def ensure_model(self, name: str, model_id: str) -> Provider:
+        """Ensure *model_id* exists under ``providers[name].models`` (in memory).
+
+        Does not write the TOML file unless the caller invokes :meth:`write`.
+        """
+        mid = model_id.strip()
+        if not mid:
+            msg = "model id must not be empty"
+            raise ValueError(msg)
+        provider = self._take_provider(name)
+        if mid in provider.models:
+            return provider
+        models = dict(provider.models)
+        models[mid] = ModelConfig()
+        updated = msgspec.structs.replace(provider, models=models)
+        self._providers[name] = updated
+        return updated
+
+    def merge_models(self, name: str, model_ids: Sequence[str]) -> Provider:
+        """Union *model_ids* into the provider catalog (keep existing configs).
+
+        Does not write the TOML file unless the caller invokes :meth:`write`.
+        """
+        provider = self._take_provider(name)
+        models = dict(provider.models)
+        added = False
+        for raw in model_ids:
+            mid = raw.strip() if raw else ""
+            if not mid or mid in models:
+                continue
+            models[mid] = ModelConfig()
+            added = True
+        if not added and models:
+            return provider
+        if not models:
+            msg = f"cannot merge models for provider {name!r}: no model ids"
+            raise ValueError(msg)
+        updated = msgspec.structs.replace(provider, models=models)
+        self._providers[name] = updated
+        return updated
+
     # -- persistence --
 
     def write(self) -> None:

src/plyngent/memory/database/schema.py

@@ -32,6 +32,8 @@ class Session(PlyngentBase):
     # Last selected provider/model for this session (config provider key + model id).
     provider_name: Mapped[str | None] = mapped_column(String(128), nullable=True)
     model: Mapped[str | None] = mapped_column(String(256), nullable=True)
+    # Todo/task stack JSON for multi-step sub-tasks (optional).
+    todo_stack: Mapped[dict[str, object] | None] = mapped_column(JSON(), nullable=True)
     created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), server_default=func.now())
     updated_at: Mapped[datetime] = mapped_column(
         DateTime(timezone=True), server_default=func.now(), onupdate=func.now()

src/plyngent/memory/database/store.py

@@ -2,7 +2,7 @@ from __future__ import annotations
 
 from datetime import UTC, datetime
 from pathlib import Path
-from typing import TYPE_CHECKING, Self
+from typing import TYPE_CHECKING, Self, cast
 
 import msgspec
 from sqlalchemy import delete, select, text
@@ -68,6 +68,7 @@ class MemoryStore:
             _ = await conn.run_sync(PlyngentBase.metadata.create_all)
             await conn.run_sync(_migrate_session_workspace)
             await conn.run_sync(_migrate_session_llm)
+            await conn.run_sync(_migrate_session_todo_stack)
 
     async def close(self) -> None:
         """Dispose the underlying engine."""
@@ -208,6 +209,31 @@ class MemoryStore:
             await session.refresh(row)
             return row
 
+    async def get_session_todo_stack(self, sid: int) -> dict[str, object] | None:
+        """Return the stored todo stack JSON for *sid*, or None."""
+        async with self._session_factory() as session:
+            row = await session.get(Session, sid)
+            if row is None:
+                msg = f"session not found: {sid}"
+                raise ValueError(msg)
+            raw = row.todo_stack
+            if raw is None:
+                return None
+            return {str(k): v for k, v in cast("dict[object, object]", raw).items()}
+
+    async def update_session_todo_stack(self, sid: int, data: dict[str, object] | None) -> Session:
+        """Persist todo stack JSON for a session (None clears)."""
+        async with self._session_factory() as session:
+            row = await session.get(Session, sid)
+            if row is None:
+                msg = f"session not found: {sid}"
+                raise ValueError(msg)
+            row.todo_stack = data
+            row.updated_at = datetime.now(UTC)
+            await session.commit()
+            await session.refresh(row)
+            return row
+
     async def rename_session(self, sid: int, name: str) -> Session:
         """Rename a session (max 64 characters, non-empty after strip)."""
         cleaned = name.strip()
@@ -308,3 +334,14 @@ def _migrate_session_llm(sync_conn: object) -> None:
         _ = sync_conn.execute(text("ALTER TABLE session ADD COLUMN provider_name VARCHAR(128)"))
     if "model" not in columns:
         _ = sync_conn.execute(text("ALTER TABLE session ADD COLUMN model VARCHAR(256)"))
+
+
+def _migrate_session_todo_stack(sync_conn: object) -> None:
+    """Add ``session.todo_stack`` JSON for the todo/task sub-task stack."""
+    from sqlalchemy.engine import Connection
+
+    if not isinstance(sync_conn, Connection):
+        return
+    columns = _session_columns(sync_conn)
+    if "todo_stack" not in columns:
+        _ = sync_conn.execute(text("ALTER TABLE session ADD COLUMN todo_stack JSON"))

src/plyngent/tools/__init__.py

@@ -21,6 +21,17 @@ from .process import open_pty as open_pty
 from .process import read_pty as read_pty
 from .process import run_command as run_command
 from .process import write_pty as write_pty
+from .process import write_pty_keys as write_pty_keys
+from .temp_workspace import cleanup_temporary_workspaces as cleanup_temporary_workspaces
+from .temp_workspace import new_temporary_workspace as new_temporary_workspace
+from .todo import TODO_TOOLS as TODO_TOOLS
+from .todo import get_todo_stack as get_todo_stack
+from .todo import set_todo_stack as set_todo_stack
+from .todo import todo_clear as todo_clear
+from .todo import todo_list as todo_list
+from .todo import todo_pop as todo_pop
+from .todo import todo_push as todo_push
+from .todo import todo_update as todo_update
 from .vcs import VCS_TOOLS as VCS_TOOLS
 from .vcs import vcs_branch as vcs_branch
 from .vcs import vcs_diff as vcs_diff
@@ -31,14 +42,19 @@ from .workspace import (
     DEFAULT_COMMAND_DENYLIST as DEFAULT_COMMAND_DENYLIST,
 )
 from .workspace import WorkspaceError as WorkspaceError
+from .workspace import add_workspace_allowlist as add_workspace_allowlist
 from .workspace import check_command_allowed as check_command_allowed
+from .workspace import clear_workspace_allowlist as clear_workspace_allowlist
 from .workspace import clear_workspace_root as clear_workspace_root
 from .workspace import get_command_denylist as get_command_denylist
 from .workspace import get_path_denylist as get_path_denylist
 from .workspace import get_workspace_root as get_workspace_root
+from .workspace import list_workspace_allowlist as list_workspace_allowlist
+from .workspace import pop_owned_temporary_workspaces as pop_owned_temporary_workspaces
+from .workspace import remove_workspace_allowlist as remove_workspace_allowlist
 from .workspace import resolve_path as resolve_path
 from .workspace import set_command_denylist as set_command_denylist
 from .workspace import set_path_denylist as set_path_denylist
 from .workspace import set_workspace_root as set_workspace_root
 
-DEFAULT_TOOLS = [*FILE_TOOLS, *PROCESS_TOOLS, *VCS_TOOLS, *CHAT_TOOLS]
+DEFAULT_TOOLS = [*FILE_TOOLS, *PROCESS_TOOLS, *VCS_TOOLS, *CHAT_TOOLS, *TODO_TOOLS]

src/plyngent/tools/danger.py

@@ -1,11 +1,111 @@
 from __future__ import annotations
 
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, cast
 
 from plyngent.tools.workspace import WorkspaceError, resolve_path
 
 if TYPE_CHECKING:
-    from collections.abc import Mapping
+    from collections.abc import Mapping, Sequence
+
+_DISPLAY_ARGV_MAX = 400
+_CODE_PREVIEW_MAX = 240
+
+_SHELL_BASENAMES: frozenset[str] = frozenset(
+    {
+        "bash",
+        "sh",
+        "zsh",
+        "fish",
+        "dash",
+        "ksh",
+        "csh",
+        "tcsh",
+        "powershell",
+        "pwsh",
+        "cmd",
+        "cmd.exe",
+        "python",
+        "python3",
+        "python2",
+        "ipython",
+        "ipython3",
+        "node",
+        "nodejs",
+        "deno",
+        "bun",
+        "ruby",
+        "perl",
+        "php",
+        "lua",
+        "r",
+        "julia",
+        "irb",
+        "pry",
+        "ghci",
+        "scala",
+        "jshell",
+        "sqlite3",
+        "psql",
+        "mysql",
+        "mongo",
+        "redis-cli",
+    }
+)
+
+
+def _basename(argv0: str) -> str:
+    name = argv0.replace("\\", "/").rsplit("/", 1)[-1]
+    name = name.removesuffix(".exe")
+    return name.lower()
+
+
+def _as_argv(args: Mapping[str, object]) -> list[str] | None:
+    command = args.get("command")
+    if not isinstance(command, list) or not command:
+        return None
+    out: list[str] = []
+    for part_obj in cast("list[object]", command):
+        if not isinstance(part_obj, str):
+            return None
+        out.append(part_obj)
+    return out
+
+
+def _find_dash_c_code(argv: Sequence[str]) -> str | None:
+    """Return the argument after ``-c`` / ``-c…`` if present (python/bash/node style)."""
+    for index, part in enumerate(argv[1:], start=1):
+        if part == "-c":
+            return argv[index + 1] if index + 1 < len(argv) else ""
+        # Combined short forms are uncommon; only exact -c is supported.
+    return None
+
+
+def _shell_or_dash_c_reason(argv: Sequence[str], *, via: str) -> str | None:
+    """Confirm interactive shells/REPLs and ``-c`` one-liners so the user can inspect argv.
+
+    Multi-line reason (shown inside the CLI confirm box). ``via`` is a short
+    label (tool name), not repeated on every line.
+    """
+    if not argv:
+        return None
+    base = _basename(argv[0])
+    display = " ".join(argv)
+    if len(display) > _DISPLAY_ARGV_MAX:
+        display = display[:_DISPLAY_ARGV_MAX] + "…"
+
+    code = _find_dash_c_code(argv)
+    if code is not None:
+        preview = code if len(code) <= _CODE_PREVIEW_MAX else code[:_CODE_PREVIEW_MAX] + "…"
+        return f"{via}: {base} -c (review code before allow)\nargv:\n  {display}\n-c code:\n  {preview}"
+
+    if base in _SHELL_BASENAMES and len(argv) == 1:
+        return f"{via}: interactive {base!r} (review before allow)\nargv:\n  {display}"
+
+    # e.g. python -i, bash --login without -c still needs a glance.
+    if base in _SHELL_BASENAMES:
+        return f"{via}: shell/runtime {base!r} (review before allow)\nargv:\n  {display}"
+
+    return None
 
 
 def _write_file_reason(args: Mapping[str, object]) -> str | None:
@@ -15,32 +115,80 @@ def _write_file_reason(args: Mapping[str, object]) -> str | None:
     try:
         target = resolve_path(path)
     except WorkspaceError:
-        return None
-    if target.exists() or target.is_symlink():
-        return f"overwrite existing file {path!r}"
-    return None
+        return f"write file {path!r}"
+    return f"write file {path!r} ({target})"
 
 
-def classify_danger(name: str, args: Mapping[str, object]) -> str | None:
+def _edit_replace_reason(args: Mapping[str, object]) -> str | None:
+    path = args.get("path")
+    if not isinstance(path, str) or not path:
+        return None
+    return f"edit (replace) in {path!r}"
+
+
+def _edit_lineno_reason(args: Mapping[str, object]) -> str | None:
+    path = args.get("path")
+    if not isinstance(path, str) or not path:
+        return None
+    start = args.get("start_line")
+    end = args.get("end_line")
+    return f"edit lines {start}-{end} in {path!r}"
+
+
+def _copy_path_reason(args: Mapping[str, object]) -> str | None:
+    src = args.get("src")
+    dst = args.get("dst")
+    return f"copy {src!r} → {dst!r}"
+
+
+def _move_path_reason(args: Mapping[str, object]) -> str | None:
+    src = args.get("src")
+    dst = args.get("dst")
+    return f"move {src!r} → {dst!r}"
+
+
+def _delete_path_reason(args: Mapping[str, object]) -> str | None:
+    path = args.get("path")
+    recursive = bool(args.get("recursive", False))
+    extra = " recursively" if recursive else ""
+    return f"delete path {path!r}{extra}"
+
+
+def _run_command_reason(args: Mapping[str, object]) -> str | None:
+    argv = _as_argv(args)
+    if argv is None:
+        return None
+    return _shell_or_dash_c_reason(argv, via="run_command")
+
+
+def _open_pty_reason(args: Mapping[str, object]) -> str | None:
+    argv = _as_argv(args)
+    if argv is None:
+        return None
+    return _shell_or_dash_c_reason(argv, via="open_pty")
+
+
+def classify_danger(name: str, args: Mapping[str, object]) -> str | None:  # noqa: PLR0911
     """Return a short reason if ``name``/``args`` need user confirm, else ``None``.
 
     Hard denylists (paths/commands) still raise independently. This only covers
-    soft confirms for mutating tools that policy otherwise allows.
+    soft confirms for mutating tools and risky shell/REPL launches
+    (interactive shells and ``python -c`` / ``bash -c`` one-liners).
     """
-    reasons: dict[str, str | None] = {
-        "delete_path": (
-            f"delete path {args.get('path', '')!r} recursively"
-            if bool(args.get("recursive", False))
-            else f"delete path {args.get('path', '')!r}"
-        ),
-        "move_path": f"move {args.get('src', '')!r} -> {args.get('dst', '')!r}",
-        "copy_path": (
-            f"copy with overwrite {args.get('src', '')!r} -> {args.get('dst', '')!r}"
-            if bool(args.get("overwrite", False))
-            else None
-        ),
-        "write_file": _write_file_reason(args),
-    }
-    if name not in reasons:
+    if name == "delete_path":
+        return _delete_path_reason(args)
+    if name == "move_path":
+        return _move_path_reason(args)
+    if name == "copy_path":
+        return _copy_path_reason(args)
+    if name == "write_file":
+        return _write_file_reason(args)
+    if name == "edit_replace":
+        return _edit_replace_reason(args)
+    if name == "edit_lineno":
+        return _edit_lineno_reason(args)
+    if name == "run_command":
+        return _run_command_reason(args)
+    if name == "open_pty":
+        return _open_pty_reason(args)
     return None
-    return reasons[name]

src/plyngent/tools/file/__init__.py

@@ -1,3 +1,5 @@
+from plyngent.tools.temp_workspace import new_temporary_workspace as new_temporary_workspace
+
 from .edit_lineno import edit_lineno as edit_lineno
 from .edit_replace import edit_replace as edit_replace
 from .fs_ops import copy_path as copy_path
@@ -22,4 +24,5 @@ FILE_TOOLS = [
     copy_path,
     move_path,
     delete_path,
+    new_temporary_workspace,
 ]

src/plyngent/tools/file/read.py

@@ -3,12 +3,33 @@ from __future__ import annotations
 from plyngent.agent import tool
 from plyngent.tools.workspace import resolve_path
 
+_LINENO_WIDTH = 6
+
+
+def _format_with_lineno(lines: list[str], *, start_lineno: int) -> str:
+    """Prefix each line with a 1-based absolute line number (``edit_lineno`` style)."""
+    out: list[str] = []
+    for index, line in enumerate(lines):
+        lineno = start_lineno + index
+        # Strip keepends for the body; re-add a single newline after the prefix.
+        body = line.rstrip("\r\n")
+        out.append(f"{lineno:>{_LINENO_WIDTH}}|{body}\n")
+    return "".join(out)
+
 
 @tool
-def read_file(path: str, *, offset: int = 0, limit: int | None = None) -> str:
+def read_file(
+    path: str,
+    *,
+    offset: int = 0,
+    limit: int | None = None,
+    with_lineno: bool = False,
+) -> str:
     """Read a text file under the workspace.
 
     ``offset`` is 0-based line start; ``limit`` is max lines (None = rest of file).
+    When ``with_lineno`` is true, each line is prefixed with its 1-based file line
+    number (``     N|…``), matching ``edit_lineno`` numbering.
     """
     target = resolve_path(path)
     if not target.is_file():
@@ -21,4 +42,7 @@ def read_file(path: str, *, offset: int = 0, limit: int | None = None) -> str:
     end = len(lines) if limit is None else min(len(lines), start + limit)
     if start >= len(lines):
         return ""
-    return "".join(lines[start:end])
+    slice_lines = lines[start:end]
+    if with_lineno:
+        return _format_with_lineno(slice_lines, start_lineno=start + 1)
+    return "".join(slice_lines)

src/plyngent/tools/file/tree.py

@@ -4,9 +4,10 @@ from dataclasses import dataclass
 from typing import TYPE_CHECKING
 
 from plyngent.agent import tool
-from plyngent.tools.workspace import WorkspaceError, resolve_path
+from plyngent.tools.workspace import WorkspaceError, get_path_denylist, resolve_path
 
 if TYPE_CHECKING:
+    from collections.abc import Sequence
     from pathlib import Path
 
 DEFAULT_MAX_DEPTH = 4
@@ -26,21 +27,58 @@ VCS_DIR_NAMES: frozenset[str] = frozenset(
     }
 )
 
+# Extra noise dirs skipped by default (in addition to VCS / optional hidden).
+# Pass skip_dirs=[] to disable this list (VCS still always skipped).
+DEFAULT_NOISE_DIR_NAMES: frozenset[str] = frozenset(
+    {
+        "node_modules",
+        "__pycache__",
+        ".venv",
+        "venv",
+        "dist",
+        "build",
+        "target",
+        ".tox",
+        ".mypy_cache",
+        ".ruff_cache",
+        ".pytest_cache",
+        "coverage",
+        ".next",
+        ".nuxt",
+        ".turbo",
+        ".cache",
+        "eggs",
+        ".eggs",
+        "htmlcov",
+    }
+)
+
 
 @dataclass(frozen=True, slots=True)
 class _TreeLimits:
     max_depth: int
     max_entries: int
     skip_hidden_dirs: bool
+    skip_basenames: frozenset[str]
+    apply_path_denylist: bool
 
 
-def _skip_directory(name: str, *, skip_hidden_dirs: bool) -> bool:
-    if name in VCS_DIR_NAMES:
+def _skip_directory(name: str, *, limits: _TreeLimits) -> bool:
+    if name in VCS_DIR_NAMES or name in limits.skip_basenames:
         return True
-    return bool(skip_hidden_dirs and name.startswith("."))
+    return bool(limits.skip_hidden_dirs and name.startswith("."))
 
 
-def _list_children(directory: Path, *, skip_hidden_dirs: bool) -> list[Path] | str:
+def _path_denied(path: Path) -> bool:
+    """True when resolved path matches a path_denylist substring."""
+    denylist = get_path_denylist()
+    if not denylist:
+        return False
+    resolved_str = str(path).replace("\\", "/")
+    return any(pattern and pattern.replace("\\", "/") in resolved_str for pattern in denylist)
+
+
+def _list_children(directory: Path, *, limits: _TreeLimits) -> list[Path] | str:
     try:
         children = list(directory.iterdir())
     except OSError as exc:
@@ -51,7 +89,9 @@ def _list_children(directory: Path, *, skip_hidden_dirs: bool) -> list[Path] | s
             is_dir = child.is_dir()
         except OSError:
             continue
-        if is_dir and _skip_directory(child.name, skip_hidden_dirs=skip_hidden_dirs):
+        if is_dir and _skip_directory(child.name, limits=limits):
+            continue
+        if limits.apply_path_denylist and _path_denied(child):
             continue
         visible.append(child)
     # Directories first, then files; alphabetical within each group.
@@ -70,7 +110,7 @@ def _render_tree(
     if depth >= limits.max_depth:
         return
 
-    children = _list_children(directory, skip_hidden_dirs=limits.skip_hidden_dirs)
+    children = _list_children(directory, limits=limits)
     if isinstance(children, str):
         lines.append(f"{prefix}{children}")
         return
@@ -104,6 +144,13 @@ def _render_tree(
         lines.append(f"{prefix}└── … ({more} more entries not shown)")
 
 
+def _resolve_skip_basenames(skip_dirs: Sequence[str] | None) -> frozenset[str]:
+    """None → default noise set; explicit list (including empty) replaces defaults."""
+    if skip_dirs is None:
+        return DEFAULT_NOISE_DIR_NAMES
+    return frozenset(name for name in skip_dirs if name)
+
+
 @tool
 def tree(
     path: str = ".",
@@ -111,13 +158,22 @@ def tree(
     max_depth: int = DEFAULT_MAX_DEPTH,
     max_entries: int = DEFAULT_MAX_ENTRIES,
     skip_hidden_dirs: bool = True,
+    skip_dirs: list[str] | None = None,
+    apply_path_denylist: bool = True,
 ) -> str:
     """Show a directory tree under the workspace.
 
     Always skips VCS metadata directories (``.git``, ``.hg``, ``.svn``, …).
+    By default also skips common noise dirs (``node_modules``, ``__pycache__``,
+    ``.venv``, ``dist``, …). Pass ``skip_dirs=[]`` to disable the noise list
+    (VCS still skipped). Pass an explicit list to replace the default noise set.
+
     By default skips other dot-directories (not hidden files). Use
     ``skip_hidden_dirs=false`` to include them.
 
+    ``apply_path_denylist`` (default true) hides entries whose full path matches
+    the agent ``path_denylist`` policy.
+
     ``max_depth`` limits how deep directories are expanded (1 = origin + children).
     ``max_entries`` caps how many entries are listed per directory.
     """
@@ -135,15 +191,18 @@ def tree(
 
     root_label = path.rstrip("/\\") or "."
     lines = [f"{root_label}/"]
-    _render_tree(
-        origin,
-        prefix="",
-        depth=0,
     limits = _TreeLimits(
         max_depth=max_depth,
         max_entries=max_entries,
         skip_hidden_dirs=skip_hidden_dirs,
-        ),
+        skip_basenames=_resolve_skip_basenames(skip_dirs),
+        apply_path_denylist=apply_path_denylist,
+    )
+    _render_tree(
+        origin,
+        prefix="",
+        depth=0,
+        limits=limits,
         lines=lines,
     )
     return "\n".join(lines)

src/plyngent/tools/process/__init__.py

@@ -1,7 +1,10 @@
 from .close_pty import close_pty as close_pty
 from .open_pty import open_pty as open_pty
+from .pty_terminal import decode_write_data as decode_write_data
+from .pty_terminal import sanitize_pty_output_for_tool as sanitize_pty_output_for_tool
 from .read_pty import read_pty as read_pty
 from .run_command import run_command as run_command
 from .write_pty import write_pty as write_pty
+from .write_pty_keys import write_pty_keys as write_pty_keys
 
-PROCESS_TOOLS = [run_command, open_pty, read_pty, write_pty, close_pty]
+PROCESS_TOOLS = [run_command, open_pty, read_pty, write_pty, write_pty_keys, close_pty]

src/plyngent/tools/process/pty_session.py

@@ -8,6 +8,7 @@ from threading import Lock
 from typing import TYPE_CHECKING, ClassVar
 
 from plyngent.tools.process.pty_backend import PtyHandle, pty_available, spawn_pty
+from plyngent.tools.process.pty_terminal import sanitize_pty_output_for_tool
 from plyngent.tools.workspace import WorkspaceError, check_command_allowed, resolve_path
 
 if TYPE_CHECKING:
@@ -286,6 +287,8 @@ class PtyManager:
         truncated = len(data) > max_bytes
         if truncated:
             data = data[:max_bytes]
+        # Escape CSI so tool results echoed to the host TTY cannot reprogram it.
+        data = sanitize_pty_output_for_tool(data)
         budget_exhausted = cls._maybe_raise_budget(session)
         return PtyReadResult(
             session_id=session_id,
@@ -354,6 +357,8 @@ class PtyManager:
         with cls._lock:
             _ = cls._sessions.pop(session_id, None)
 
+        # No host TTY reset: tool-facing read_pty sanitizes CSI so chat echo
+        # cannot reprogram the user terminal.
         return PtyCloseResult(
             session_id=session_id,
             closed=True,
@@ -381,6 +386,7 @@ class PtyManager:
 
     @classmethod
     def close_all(cls) -> None:
+        """Close every open session (no host TTY reset)."""
         with cls._lock:
             ids = list(cls._sessions.keys())
         for session_id in ids:

src/plyngent/tools/process/pty_terminal.py

@@ -0,0 +1,108 @@
+"""PTY payload helpers for agent tools.
+
+Child PTY I/O stays on the master FD. Tool results are printed on the *user*
+TTY by the CLI, so any CSI/control bytes in ``read_pty`` data would reprogram
+the host terminal. We sanitize on the tool boundary instead of resetting the
+host after close (which flashes the screen on every chat exit).
+"""
+
+from __future__ import annotations
+
+import re
+
+# Match common \xNN / \uNNNN / named ctrl+ / esc sequences in write_pty_keys data.
+_HEX_BYTE = re.compile(r"\\x([0-9A-Fa-f]{2})")
+_HEX_U = re.compile(r"\\u([0-9A-Fa-f]{4})")
+_CTRL = re.compile(r"ctrl\+([a-z@\[\\\]\^_])", re.IGNORECASE)
+_KEY = re.compile(r"key=(esc|escape|enter|tab|up|down|left|right)", re.IGNORECASE)
+_SIMPLE = {
+    r"\n": "\n",
+    r"\r": "\r",
+    r"\t": "\t",
+    r"\e": "\x1b",
+    r"\E": "\x1b",
+    r"\0": "\x00",
+}
+
+_KEY_MAP = {
+    "esc": "\x1b",
+    "escape": "\x1b",
+    "enter": "\r",
+    "tab": "\t",
+    "up": "\x1b[A",
+    "down": "\x1b[B",
+    "right": "\x1b[C",
+    "left": "\x1b[D",
+}
+_SIMPLE_ESCAPE_LEN = 2
+
+# C0 controls except TAB/LF/CR (those stay for readable logs).
+_UNSAFE_CTRL = re.compile(r"[\x00-\x08\x0b\x0c\x0e-\x1f\x7f]")
+
+
+def sanitize_pty_output_for_tool(data: str) -> str:
+    """Make PTY bytes safe to print on the host as tool/chat text.
+
+    - ESC becomes the two-character sequence ``\\\\x1b`` so CSI is not executed
+      when the CLI echoes tool results.
+    - Other C0 controls (except tab/LF/CR) become ``\\\\xHH``.
+    """
+    if not data:
+        return data
+
+    def _esc_ctrl(match: re.Match[str]) -> str:
+        return f"\\x{ord(match.group(0)):02x}"
+
+    # ESC first as a stable, readable form used in docs/tests.
+    out = data.replace("\x1b", "\\x1b")
+    return _UNSAFE_CTRL.sub(_esc_ctrl, out)
+
+
+def decode_write_data(data: str) -> str:
+    """Expand agent-friendly escapes into raw PTY input (for ``write_pty_keys`` only).
+
+    Supported (as literal characters in ``data``):
+
+    - ``\\n`` ``\\r`` ``\\t`` ``\\e`` / ``\\E`` (ESC) ``\\0``
+    - ``\\xHH`` byte, ``\\uHHHH`` Unicode code point
+    - ``ctrl+c`` / ``ctrl+x`` ... (case-insensitive; A-Z or @ [ \\ ] ^ _)
+    - ``key=esc`` ``key=enter`` ``key=tab`` ``key=up|down|left|right``
+    """
+    if not data:
+        return data
+
+    out: list[str] = []
+    i = 0
+    n = len(data)
+    while i < n:
+        rest = data[i:]
+        m_key = _KEY.match(rest)
+        if m_key is not None:
+            out.append(_KEY_MAP[m_key.group(1).lower()])
+            i += m_key.end()
+            continue
+        m_ctrl = _CTRL.match(rest)
+        if m_ctrl is not None:
+            ch = m_ctrl.group(1).upper()
+            out.append(chr((ord(ch) - ord("@")) & 0x1F))
+            i += m_ctrl.end()
+            continue
+        m_hex = _HEX_BYTE.match(rest)
+        if m_hex is not None:
+            out.append(chr(int(m_hex.group(1), 16)))
+            i += m_hex.end()
+            continue
+        m_u = _HEX_U.match(rest)
+        if m_u is not None:
+            out.append(chr(int(m_u.group(1), 16)))
+            i += m_u.end()
+            continue
+        if rest.startswith("\\") and len(rest) >= _SIMPLE_ESCAPE_LEN:
+            pair = rest[:_SIMPLE_ESCAPE_LEN]
+            if pair in _SIMPLE:
+                out.append(_SIMPLE[pair])
+                i += _SIMPLE_ESCAPE_LEN
+                continue
+        out.append(data[i])
+        i += 1
+    return "".join(out)

src/plyngent/tools/process/write_pty.py

@@ -6,22 +6,31 @@ from plyngent.tools.workspace import WorkspaceError
 from .pty_session import PtyManager
 
 
-@tool
-def write_pty(session_id: int, data: str) -> str:
-    """Write text to a PTY session (interactive input). Does not append a newline."""
-    try:
-        PtyManager.write(session_id, data)
+def write_pty_payload(session_id: int, raw: str) -> str:
+    """Write raw bytes (as str) to the PTY and format the tool status string."""
+    PtyManager.write(session_id, raw)
     session = PtyManager.refresh(session_id)
-    except WorkspaceError as exc:
-        return f"error: {exc}"
-    except OSError as exc:
-        return f"error: failed to write PTY: {exc}"
     exit_disp = "" if session.exit_code is None else str(session.exit_code)
     return "\n".join(
         [
             f"session_id={session_id}",
             f"alive={'true' if session.alive else 'false'}",
             f"exit_code={exit_disp}",
-            f"wrote={len(data)}",
+            f"wrote={len(raw.encode())}",
         ]
     )
+
+
+@tool
+def write_pty(session_id: int, data: str) -> str:
+    """Write **literal** text to a PTY session. Does not append a newline.
+
+    ``data`` is sent unchanged (no ``ctrl+x`` / ``\\\\xHH`` expansion). For
+    control sequences use :func:`write_pty_keys`.
+    """
+    try:
+        return write_pty_payload(session_id, data)
+    except WorkspaceError as exc:
+        return f"error: {exc}"
+    except OSError as exc:
+        return f"error: failed to write PTY: {exc}"

src/plyngent/tools/process/write_pty_keys.py

@@ -0,0 +1,30 @@
+from __future__ import annotations
+
+from plyngent.agent import tool
+from plyngent.tools.workspace import WorkspaceError
+
+from .pty_terminal import decode_write_data
+from .write_pty import write_pty_payload
+
+
+@tool
+def write_pty_keys(session_id: int, data: str) -> str:
+    """Write to a PTY after expanding key escapes (never for normal typing).
+
+    Use this only for control sequences. Prefer :func:`write_pty` for plain text
+    so strings like ``press ctrl+c`` are not rewritten.
+
+    Escapes (literal characters in ``data``):
+
+    - ``\\\\n`` ``\\\\r`` ``\\\\t`` ``\\\\e``/``\\\\E`` (ESC) ``\\\\0``
+    - ``\\\\xHH`` byte, ``\\\\uHHHH`` Unicode code point
+    - ``ctrl+c`` / ``ctrl+x`` ... (case-insensitive)
+    - ``key=esc|enter|tab|up|down|left|right``
+    """
+    try:
+        raw = decode_write_data(data)
+        return write_pty_payload(session_id, raw)
+    except WorkspaceError as exc:
+        return f"error: {exc}"
+    except OSError as exc:
+        return f"error: failed to write PTY: {exc}"

src/plyngent/tools/temp_workspace.py

@@ -0,0 +1,96 @@
+from __future__ import annotations
+
+import re
+import shutil
+import tempfile
+from pathlib import Path
+
+from plyngent.agent import tool
+from plyngent.tools.workspace import (
+    MAX_TEMPORARY_WORKSPACES,
+    WorkspaceError,
+    add_workspace_allowlist,
+    list_workspace_allowlist,
+    pop_owned_temporary_workspaces,
+    remove_workspace_allowlist,
+)
+
+_DEFAULT_PREFIX = "ws"
+_PREFIX_MAX_LEN = 32
+_PREFIX_SAFE = re.compile(rf"^[A-Za-z0-9_-]{{1,{_PREFIX_MAX_LEN}}}$")
+
+
+def _sanitize_prefix(prefix: str) -> str:
+    token = (prefix or _DEFAULT_PREFIX).strip() or _DEFAULT_PREFIX
+    # Replace unsafe characters so mkdtemp stays portable on Windows/POSIX.
+    cleaned = re.sub(r"[^A-Za-z0-9_-]+", "-", token)
+    cleaned = cleaned.strip("-_") or _DEFAULT_PREFIX
+    if len(cleaned) > _PREFIX_MAX_LEN:
+        cleaned = cleaned[:_PREFIX_MAX_LEN]
+    if not _PREFIX_SAFE.match(cleaned):
+        return _DEFAULT_PREFIX
+    return cleaned
+
+
+def _is_under_system_temp(path: Path) -> bool:
+    """True if *path* is under the OS temporary directory (safe to rmtree)."""
+    try:
+        temp_root = Path(tempfile.gettempdir()).expanduser().resolve()
+        resolved = path.expanduser().resolve()
+        _ = resolved.relative_to(temp_root)
+    except OSError, ValueError:
+        return False
+    return True
+
+
+def cleanup_temporary_workspaces() -> int:
+    """Remove directories created by :func:`new_temporary_workspace` (chat exit).
+
+    Only deletes paths still under the system temp dir. Returns the number of
+    directories removed.
+    """
+    removed = 0
+    for path in pop_owned_temporary_workspaces():
+        if not _is_under_system_temp(path):
+            remove_workspace_allowlist(path)
+            continue
+        if path.is_dir():
+            shutil.rmtree(path, ignore_errors=True)
+            removed += 1
+        remove_workspace_allowlist(path)
+    return removed
+
+
+@tool
+def new_temporary_workspace(prefix: str = "ws") -> str:
+    """Create a scratch directory under the system temp dir and allow tool paths in it.
+
+    The project workspace is unchanged: relative paths still resolve there.
+    Use the returned **absolute** path for file/process tools. Temporary
+    workspaces are deleted when this chat process exits (not on each turn).
+
+    Cross-platform (uses ``tempfile``; typically ``/tmp`` on POSIX, ``%TEMP%``
+    on Windows). At most 16 concurrent temporary workspaces per process.
+    """
+    if len(list_workspace_allowlist()) >= MAX_TEMPORARY_WORKSPACES:
+        return f"error: too many temporary workspaces (max {MAX_TEMPORARY_WORKSPACES})"
+
+    safe = _sanitize_prefix(prefix)
+    try:
+        # mkdtemp is cross-platform; prefix must end with - for readability.
+        path_str = tempfile.mkdtemp(prefix=f"plyngent-{safe}-")
+        path = Path(path_str).resolve()
+    except OSError as exc:
+        return f"error: failed to create temporary workspace: {exc}"
+
+    try:
+        _ = add_workspace_allowlist(path, owned=True)
+    except WorkspaceError as exc:
+        shutil.rmtree(path, ignore_errors=True)
+        return f"error: {exc}"
+
+    return (
+        f"temporary_workspace={path}\n"
+        "note: project workspace unchanged; use this absolute path for tools; "
+        "removed when chat exits"
+    )

src/plyngent/tools/todo.py

@@ -0,0 +1,126 @@
+from __future__ import annotations
+
+from typing import TYPE_CHECKING, cast
+
+from plyngent.agent import tool
+
+if TYPE_CHECKING:
+    from collections.abc import Callable
+
+    from plyngent.agent.todo_stack import TodoStack, TodoStatus
+
+_stack: TodoStack | None = None
+_on_change: Callable[[], None] | None = None
+
+_VALID_STATUS = frozenset({"pending", "in_progress", "done", "cancelled"})
+
+
+def set_todo_stack(stack: TodoStack | None, *, on_change: Callable[[], None] | None = None) -> None:
+    """Bind the session todo stack for tool handlers (and optional persist hook)."""
+    global _stack, _on_change  # noqa: PLW0603 — intentional process bind
+    _stack = stack
+    _on_change = on_change
+
+
+def get_todo_stack() -> TodoStack | None:
+    return _stack
+
+
+def _require_stack() -> TodoStack:
+    if _stack is None:
+        msg = "todo stack is not available in this session"
+        raise RuntimeError(msg)
+    return _stack
+
+
+def _notify() -> None:
+    if _on_change is not None:
+        _on_change()
+
+
+@tool(name="todo_list")
+def todo_list() -> str:
+    """Show the LIFO stack of **task groups** (TOP group = current breakdown level).
+
+    Push creates one group of siblings; pop removes the whole top group.
+    Pattern: push [T1,T2] → push [T1.1,T1.2] → finish children → pop → push [T2.1]…
+    """
+    stack = _require_stack()
+    stack.mark_touched()
+    _notify()
+    return stack.render()
+
+
+@tool(name="todo_push")
+def todo_push(titles: list[str], notes: str = "") -> str:
+    """Push **one task group** (siblings) onto the stack — not one level per title.
+
+    ``titles``: JSON array of strings (tool schema type ``array``). All entries
+    become members of a single new TOP group. Example: ``[\"T1\", \"T2\"]`` pushes
+    one group {T1, T2}; a later ``[\"T1.1\", \"T1.2\"]`` pushes a child group above it.
+    """
+    stack = _require_stack()
+    parsed = [t.strip() for t in titles if t and t.strip()]
+    if not parsed:
+        return "error: titles must be a non-empty array of strings"
+    try:
+        group = stack.push_group(parsed, notes=notes)
+    except ValueError as exc:
+        return f"error: {exc}"
+    _notify()
+    ids = ", ".join(i.id for i in group.items)
+    return f"pushed group (depth={stack.depth}) items=[{ids}]\n{stack.render()}"
+
+
+@tool(name="todo_pop")
+def todo_pop() -> str:
+    """Pop the entire **top group** (all siblings from that push)."""
+    stack = _require_stack()
+    group = stack.pop()
+    if group is None:
+        return "todo stack empty"
+    _notify()
+    titles = ", ".join(f"{i.id}:{i.title}" for i in group.items) or "(empty)"
+    top = stack.top_group
+    top_s = "(empty)" if top is None else ", ".join(i.id for i in top.items)
+    return f"popped TOP group ({titles}); new top group=[{top_s}]\n{stack.render()}"
+
+
+@tool(name="todo_update")
+def todo_update(
+    item_id: str,
+    status: str = "",
+    title: str = "",
+    notes: str = "",
+) -> str:
+    """Update a task by id inside any group. Pop the group when that level is done."""
+    stack = _require_stack()
+    status_arg: TodoStatus | None = None
+    if status.strip():
+        token = status.strip().lower()
+        if token not in _VALID_STATUS:
+            return "error: status must be pending, in_progress, done, or cancelled"
+        status_arg = cast("TodoStatus", token)
+    try:
+        item = stack.update(
+            item_id.strip(),
+            title=title if title.strip() else None,
+            status=status_arg,
+            notes=notes if notes != "" else None,
+        )
+    except (KeyError, ValueError) as exc:
+        return f"error: {exc}"
+    _notify()
+    return f"updated {item.id} → {item.status}: {item.title}\n{stack.render()}"
+
+
+@tool(name="todo_clear")
+def todo_clear() -> str:
+    """Clear all groups on the stack."""
+    stack = _require_stack()
+    n = stack.clear()
+    _notify()
+    return f"cleared {n} item(s)"
+
+
+TODO_TOOLS = [todo_list, todo_push, todo_pop, todo_update, todo_clear]

src/plyngent/tools/workspace.py

@@ -26,6 +26,9 @@ DEFAULT_COMMAND_DENYLIST: frozenset[str] = frozenset(
     }
 )
 
+# Max concurrent temporary workspaces registered in one process.
+MAX_TEMPORARY_WORKSPACES = 16
+
 
 class WorkspaceError(ValueError):
     """Raised when a path or command violates workspace policy."""
@@ -35,6 +38,14 @@ class _WorkspaceState:
     root: Path | None = None
     path_denylist: tuple[str, ...] = ()
     command_denylist: frozenset[str] = DEFAULT_COMMAND_DENYLIST
+    # Extra roots allowed for resolve_path (e.g. temporary workspaces under system temp).
+    allowlist: list[Path]
+    # Paths created by new_temporary_workspace (subset of allowlist); cleaned on chat exit.
+    temporary_owned: list[Path]
+
+    def __init__(self) -> None:
+        self.allowlist = []
+        self.temporary_owned = []
 
 
 _state = _WorkspaceState()
@@ -59,7 +70,7 @@ def get_workspace_root() -> Path:
 
 
 def clear_workspace_root() -> None:
-    """Clear workspace root (mainly for tests)."""
+    """Clear workspace root (mainly for tests). Does not clear allowlist."""
     _state.root = None
 
 
@@ -82,18 +93,83 @@ def get_command_denylist() -> frozenset[str]:
     return _state.command_denylist
 
 
+def add_workspace_allowlist(root: Path | str, *, owned: bool = False) -> Path:
+    """Allow tool paths under *root* in addition to the primary workspace.
+
+    When *owned* is true, the path is also registered for chat-exit cleanup
+    (only paths created by :func:`new_temporary_workspace`).
+    """
+    path = Path(root).expanduser().resolve()
+    if not path.is_dir():
+        msg = f"allowlist root is not a directory: {path}"
+        raise WorkspaceError(msg)
+    if path not in _state.allowlist:
+        if len(_state.allowlist) >= MAX_TEMPORARY_WORKSPACES and owned:
+            msg = f"too many temporary workspaces (max {MAX_TEMPORARY_WORKSPACES})"
+            raise WorkspaceError(msg)
+        _state.allowlist.append(path)
+    if owned and path not in _state.temporary_owned:
+        _state.temporary_owned.append(path)
+    return path
+
+
+def list_workspace_allowlist() -> list[Path]:
+    """Return a copy of extra allowed roots (not including the primary workspace)."""
+    return list(_state.allowlist)
+
+
+def clear_workspace_allowlist() -> None:
+    """Clear allowlist and owned-temp registry (tests). Does not delete directories."""
+    _state.allowlist.clear()
+    _state.temporary_owned.clear()
+
+
+def pop_owned_temporary_workspaces() -> list[Path]:
+    """Return and clear the owned temporary workspace list (for chat-exit cleanup).
+
+    Paths remain on the allowlist until the caller removes them via
+    :func:`remove_workspace_allowlist`.
+    """
+    owned = list(_state.temporary_owned)
+    _state.temporary_owned.clear()
+    return owned
+
+
+def remove_workspace_allowlist(root: Path | str) -> None:
+    """Drop *root* from the allowlist if present."""
+    path = Path(root).expanduser().resolve()
+    while path in _state.allowlist:
+        _state.allowlist.remove(path)
+
+
+def _under_any_root(resolved: Path) -> bool:
+    roots: list[Path] = []
+    if _state.root is not None:
+        roots.append(_state.root)
+    roots.extend(_state.allowlist)
+    for root in roots:
+        try:
+            _ = resolved.relative_to(root)
+        except ValueError:
+            continue
+        return True
+    return False
+
+
 def resolve_path(path: str | Path) -> Path:
-    """Resolve ``path`` under the workspace root; reject escapes and denylist hits."""
+    """Resolve ``path`` under the workspace root or an allowlisted temp root.
+
+    Relative paths resolve against the **primary** workspace root. Absolute
+    paths may also land under a temporary workspace allowlist entry.
+    """
     root = get_workspace_root()
     candidate = Path(path)
     if not candidate.is_absolute():
         candidate = root / candidate
     resolved = candidate.expanduser().resolve()
-    try:
-        _ = resolved.relative_to(root)
-    except ValueError as exc:
+    if not _under_any_root(resolved):
         msg = f"path escapes workspace root ({root}): {path}"
-        raise WorkspaceError(msg) from exc
+        raise WorkspaceError(msg)
     # Normalize separators so denylist entries like ``/secrets/`` match on Windows.
     resolved_str = str(resolved).replace("\\", "/")
     for pattern in _state.path_denylist:

tests/test_agent/test_loop.py

@@ -30,6 +30,7 @@ from plyngent.lmproto.openai_compatible.model import (
     ChatCompletionsParam,
     ChunkChoice,
     DeltaMessage,
+    FinishReason,
     StreamFunctionDelta,
     StreamToolCallDelta,
     ToolChatMessage,
@@ -61,6 +62,28 @@ def _chunks_from_response(response: ChatCompletionResponse) -> list[ChatCompleti
                 ],
             )
         )
+    # Emit terminal finish_reason when content was streamed without one.
+    fr = response.choices[0].finish_reason
+    if (
+        fr
+        and (isinstance(message.content, str) and message.content)
+        and (message.tool_calls is UNSET or not message.tool_calls)
+    ):
+        chunks.append(
+            ChatCompletionChunk(
+                id=response.id,
+                object="chat.completion.chunk",
+                created=response.created,
+                model=response.model,
+                choices=[
+                    ChunkChoice(
+                        index=0,
+                        delta=DeltaMessage(),
+                        finish_reason=fr,
+                    )
+                ],
+            )
+        )
     tool_calls = message.tool_calls
     if tool_calls is not UNSET and tool_calls:
         deltas: list[StreamToolCallDelta] = []
@@ -152,7 +175,8 @@ class ScriptedClient:
 def _response(
     message: AssistantChatMessage,
     *,
-    usage: dict[str, int] | None = None,
+    usage: dict[str, object] | None = None,
+    finish_reason: FinishReason | None = "stop",
 ) -> ChatCompletionResponse:
     return ChatCompletionResponse(
         id="1",
@@ -164,7 +188,7 @@ def _response(
                 index=0,
                 message=message,
                 logprobs={},
-                finish_reason="stop",
+                finish_reason=finish_reason,
             )
         ],
         system_fingerprint="",
@@ -825,3 +849,118 @@ async def test_tool_result_char_budget() -> None:
     assert len(tool_msgs) == 1
     assert tool_msgs[0].content.startswith("x" * 20)
     assert "truncated" in tool_msgs[0].content
+
+
+async def test_empty_completion_raises() -> None:
+    client = ScriptedClient([_response(AssistantChatMessage(content=None))])
+    messages: list[AnyChatMessage] = [UserChatMessage(content="hi")]
+    with pytest.raises(RuntimeError, match="empty model completion"):
+        _ = [e async for e in run_chat_loop(client, messages, model="m", stream=False)]
+
+
+async def test_length_finish_raises() -> None:
+    client = ScriptedClient(
+        [
+            _response(
+                AssistantChatMessage(content="partial"),
+                finish_reason="length",
+            )
+        ]
+    )
+    messages: list[AnyChatMessage] = [UserChatMessage(content="hi")]
+    with pytest.raises(RuntimeError, match="truncated"):
+        _ = [e async for e in run_chat_loop(client, messages, model="m", stream=False)]
+
+
+async def test_content_filter_finish_raises() -> None:
+    client = ScriptedClient(
+        [
+            _response(
+                AssistantChatMessage(content=""),
+                finish_reason="content_filter",
+            )
+        ]
+    )
+    messages: list[AnyChatMessage] = [UserChatMessage(content="hi")]
+    with pytest.raises(RuntimeError, match="content filter"):
+        _ = [e async for e in run_chat_loop(client, messages, model="m", stream=False)]
+
+
+async def test_stream_missing_terminal_empty_raises() -> None:
+    class EmptyStreamClient:
+        @overload
+        async def chat_completions(
+            self, param: ChatCompletionsParam, *, stream: Literal[False] = False
+        ) -> ChatCompletionResponse: ...
+
+        @overload
+        async def chat_completions(
+            self, param: ChatCompletionsParam, *, stream: Literal[True]
+        ) -> AsyncIterator[ChatCompletionChunk]: ...
+
+        async def chat_completions(
+            self, param: ChatCompletionsParam, *, stream: bool = False
+        ) -> ChatCompletionResponse | AsyncIterator[ChatCompletionChunk]:
+            del param
+            if not stream:
+                return _response(AssistantChatMessage(content="x"))
+
+            async def chunks() -> AsyncIterator[ChatCompletionChunk]:
+                # Usage-only style chunk with no finish_reason and no content.
+                yield ChatCompletionChunk(
+                    id="1",
+                    object="chat.completion.chunk",
+                    created=0,
+                    model="t",
+                    choices=[],
+                    usage={"prompt_tokens": 1, "completion_tokens": 0, "total_tokens": 1},
+                )
+
+            return chunks()
+
+    messages: list[AnyChatMessage] = [UserChatMessage(content="hi")]
+    with pytest.raises(RuntimeError, match="stream ended without a terminal"):
+        _ = [e async for e in run_chat_loop(EmptyStreamClient(), messages, model="m", stream=True)]
+
+
+async def test_stream_payload_without_finish_reason_ok() -> None:
+    """Some providers omit finish_reason; non-empty text still counts as terminal."""
+
+    class PayloadNoFinishClient:
+        @overload
+        async def chat_completions(
+            self, param: ChatCompletionsParam, *, stream: Literal[False] = False
+        ) -> ChatCompletionResponse: ...
+
+        @overload
+        async def chat_completions(
+            self, param: ChatCompletionsParam, *, stream: Literal[True]
+        ) -> AsyncIterator[ChatCompletionChunk]: ...
+
+        async def chat_completions(
+            self, param: ChatCompletionsParam, *, stream: bool = False
+        ) -> ChatCompletionResponse | AsyncIterator[ChatCompletionChunk]:
+            del param
+            if not stream:
+                return _response(AssistantChatMessage(content="ok"))
+
+            async def chunks() -> AsyncIterator[ChatCompletionChunk]:
+                yield ChatCompletionChunk(
+                    id="1",
+                    object="chat.completion.chunk",
+                    created=0,
+                    model="t",
+                    choices=[
+                        ChunkChoice(
+                            index=0,
+                            delta=DeltaMessage(content="ok"),
+                            finish_reason=None,
+                        )
+                    ],
+                )
+
+            return chunks()
+
+    messages: list[AnyChatMessage] = [UserChatMessage(content="hi")]
+    events = [e async for e in run_chat_loop(PayloadNoFinishClient(), messages, model="m", stream=True)]
+    assert any(isinstance(e, TextDeltaEvent) and e.content == "ok" for e in events)

tests/test_agent/test_responses_bridge.py

@@ -8,6 +8,7 @@ from plyngent.agent.responses_bridge import (
     chat_param_to_responses_kwargs,
     response_to_assistant_message,
     response_to_chat_completion,
+    responses_status_to_finish_reason,
     tool_items_to_response_tools,
 )
 from plyngent.agent.responses_client import ResponsesChatClient
@@ -100,6 +101,31 @@ def test_response_to_assistant_with_tools() -> None:
     assert completion.choices[0].message.content == "done"
     assert isinstance(completion.usage, dict)
     assert completion.usage["input_tokens"] == 10
+    assert completion.choices[0].finish_reason == "tool_calls"
+
+
+def test_responses_status_to_finish_reason_incomplete() -> None:
+    body = {
+        "id": "resp_i",
+        "object": "response",
+        "created_at": 1,
+        "model": "gpt-test",
+        "status": "incomplete",
+        "incomplete_details": {"reason": "max_output_tokens"},
+        "output": [
+            {
+                "id": "msg_1",
+                "type": "message",
+                "role": "assistant",
+                "status": "incomplete",
+                "content": [{"type": "output_text", "text": "partial", "annotations": []}],
+            }
+        ],
+    }
+    resp = msgspec.convert(body, Response)
+    assert responses_status_to_finish_reason(resp, has_tool_calls=False) == "length"
+    completion = response_to_chat_completion(resp)
+    assert completion.choices[0].finish_reason == "length"
 
 
 def test_chat_param_to_responses_kwargs() -> None:

tests/test_agent/test_todo_stack.py

@@ -0,0 +1,238 @@
+from __future__ import annotations
+
+from typing import TYPE_CHECKING, Literal, overload
+
+import pytest
+
+from plyngent.agent import ChatAgent, ToolRegistry
+from plyngent.agent.todo_stack import TodoStack, parse_push_titles
+from plyngent.config.models import DatabaseConfig
+from plyngent.lmproto.openai_compatible.model import (
+    AssistantChatMessage,
+    ChatCompletionChoice,
+    ChatCompletionChunk,
+    ChatCompletionResponse,
+    ChatCompletionsParam,
+    DeveloperChatMessage,
+    UserChatMessage,
+)
+from plyngent.memory import MemoryStore
+from plyngent.tools.todo import TODO_TOOLS, set_todo_stack
+
+if TYPE_CHECKING:
+    from collections.abc import AsyncIterator
+
+
+def test_parse_push_titles() -> None:
+    assert parse_push_titles("only") == ["only"]
+    assert parse_push_titles("T1\nT2") == ["T1", "T2"]
+    assert parse_push_titles("T1; T2; T3") == ["T1", "T2", "T3"]
+    assert parse_push_titles('["A", "B"]') == ["A", "B"]
+
+
+def test_ids_reuse_after_clear() -> None:
+    stack = TodoStack()
+    g = stack.push_group(["A", "B"])
+    assert [i.id for i in g.items] == ["t1", "t2"]
+    assert stack.clear() == 2
+    g2 = stack.push_group(["C"])
+    assert [i.id for i in g2.items] == ["t1"]
+
+
+def test_ids_reuse_after_pop() -> None:
+    stack = TodoStack()
+    _ = stack.push_group(["A", "B"])  # t1, t2
+    g2 = stack.push_group(["C"])  # t3
+    assert g2.items[0].id == "t3"
+    _ = stack.pop()  # drop t3
+    g3 = stack.push_group(["D"])
+    # Highest live id is t2 → next is t3 again
+    assert g3.items[0].id == "t3"
+
+
+def test_push_is_group_not_per_task_stack() -> None:
+    """Multi-title push is one group; pop removes the whole group."""
+    stack = TodoStack()
+    g = stack.push_group(["T1", "T2"])
+    assert stack.depth == 1
+    assert [i.title for i in g.items] == ["T1", "T2"]
+    assert stack.top_group is g
+    # Not two stack levels of single tasks
+    assert len(stack.groups) == 1
+
+    g2 = stack.push_group(["T1.1", "T1.2"])
+    assert stack.depth == 2
+    assert [i.title for i in g2.items] == ["T1.1", "T1.2"]
+
+    popped = stack.pop()
+    assert popped is not None
+    assert [i.title for i in popped.items] == ["T1.1", "T1.2"]
+    assert stack.depth == 1
+    assert stack.top_group is not None
+    assert [i.title for i in stack.top_group.items] == ["T1", "T2"]
+
+
+def test_dfs_breakdown_with_groups() -> None:
+    """push [T1,T2] → push [T1.1,T1.2] → pop → push [T2.1]."""
+    stack = TodoStack()
+    root = stack.push_group(["T1", "T2"])
+    children = stack.push_group(["T1.1", "T1.2"])
+    assert stack.depth == 2
+    stack.update(children.items[0].id, status="done")
+    stack.update(children.items[1].id, status="done")
+    _ = stack.pop()
+    assert stack.depth == 1
+    stack.update(root.items[0].id, status="done")
+    _ = stack.push_group(["T2.1"])
+    assert stack.depth == 2
+    assert stack.top_group is not None
+    assert stack.top_group.items[0].title == "T2.1"
+    assert stack.groups[0].items[1].title == "T2"
+
+
+def test_single_title_still_one_group() -> None:
+    stack = TodoStack()
+    item = stack.push("only")
+    assert stack.depth == 1
+    assert item.title == "only"
+    g = stack.pop()
+    assert g is not None and len(g.items) == 1
+    assert stack.is_empty()
+
+
+def test_todo_stack_needs_review() -> None:
+    stack = TodoStack()
+    assert not stack.needs_review()
+    _ = stack.push("work")
+    stack.begin_turn()
+    assert stack.needs_review()
+    stack.mark_touched()
+    assert not stack.needs_review()
+
+
+def test_legacy_flat_and_frames_migrate() -> None:
+    flat = TodoStack.from_raw(
+        {
+            "items": [{"id": "t1", "title": "old", "status": "pending", "notes": ""}],
+            "next_id": 2,
+        }
+    )
+    assert flat.depth == 1
+    assert flat.all_items()[0].title == "old"
+
+    framed = TodoStack.from_raw(
+        {
+            "frames": [
+                {"items": [{"id": "t1", "title": "T1", "status": "pending", "notes": ""}]},
+                {"items": [{"id": "t2", "title": "T1.1", "status": "pending", "notes": ""}]},
+            ],
+            "next_id": 3,
+        }
+    )
+    assert framed.depth == 2
+    assert framed.top_group is not None
+    assert framed.top_group.items[0].title == "T1.1"
+
+
+def test_todo_stack_roundtrip_raw() -> None:
+    stack = TodoStack()
+    _ = stack.push_group(["x", "y"], notes="n")
+    raw = stack.to_raw()
+    assert "groups" in raw
+    restored = TodoStack.from_raw(raw)
+    assert restored.depth == 1
+    assert [i.title for i in restored.groups[0].items] == ["x", "y"]
+
+
+async def test_todo_tools_and_persist(tmp_path: object) -> None:
+    del tmp_path
+    memory = await MemoryStore.open(DatabaseConfig())
+    try:
+        session = await memory.create_session(name="t")
+        stack = TodoStack()
+        set_todo_stack(stack, on_change=None)
+        registry = ToolRegistry(list(TODO_TOOLS))
+        out = await registry.execute("todo_push", '{"titles": ["T1", "T2"]}')
+        assert "group" in out.lower() or "pushed" in out
+        assert stack.depth == 1
+        assert [i.title for i in stack.groups[0].items] == ["T1", "T2"]
+        out = await registry.execute("todo_push", '{"titles": ["T1", "T2"]}')
+        assert stack.depth == 2
+        out3 = await registry.execute("todo_pop", "{}")
+        assert "popped" in out3
+        assert stack.depth == 1
+        _ = await memory.update_session_todo_stack(session.sid, stack.to_raw())
+        loaded = await memory.get_session_todo_stack(session.sid)
+        assert loaded is not None
+        again = TodoStack.from_raw(loaded)
+        assert again.depth == 1
+        assert [i.title for i in again.groups[0].items] == ["T1", "T2"]
+    finally:
+        set_todo_stack(None)
+        await memory.close()
+
+
+class ScriptedClient:
+    def __init__(self) -> None:
+        self.calls = 0
+
+    @overload
+    async def chat_completions(
+        self, param: ChatCompletionsParam, *, stream: Literal[False] = False
+    ) -> ChatCompletionResponse: ...
+
+    @overload
+    async def chat_completions(
+        self, param: ChatCompletionsParam, *, stream: Literal[True]
+    ) -> AsyncIterator[ChatCompletionChunk]: ...
+
+    async def chat_completions(
+        self, param: ChatCompletionsParam, *, stream: bool = False
+    ) -> ChatCompletionResponse | AsyncIterator[ChatCompletionChunk]:
+        del stream
+        self.calls += 1
+        text = "ok" if self.calls > 1 else "done without todos"
+        for msg in param.messages:
+            if isinstance(msg, DeveloperChatMessage) and "[TODO OPEN]" in msg.content:
+                text = "reviewed stack"
+                break
+        return ChatCompletionResponse(
+            id="1",
+            object="chat.completion",
+            created=0,
+            model="m",
+            choices=[
+                ChatCompletionChoice(
+                    index=0,
+                    message=AssistantChatMessage(content=text),
+                    logprobs={},
+                    finish_reason="stop",
+                )
+            ],
+            system_fingerprint="",
+            usage={},
+        )
+
+
+@pytest.mark.asyncio
+async def test_loop_injects_todo_review_when_untouched() -> None:
+    stack = TodoStack()
+    _ = stack.push("open work")
+    stack.begin_turn()
+    client = ScriptedClient()
+    agent = ChatAgent(
+        client,  # type: ignore[arg-type]
+        model="m",
+        tools=ToolRegistry(list(TODO_TOOLS)),
+        stream=False,
+        todo_stack=stack,
+    )
+    set_todo_stack(stack)
+    try:
+        async for _event in agent.run("do stuff"):
+            pass
+        assert client.calls >= 2
+        assert any(isinstance(m, DeveloperChatMessage) and "[TODO OPEN]" in m.content for m in agent.messages)
+        assert not any(isinstance(m, UserChatMessage) and "[TODO OPEN]" in m.content for m in agent.messages)
+    finally:
+        set_todo_stack(None)

tests/test_cli/test_compact_cmd.py

@@ -99,11 +99,63 @@ async def test_compact_to_new_session(tmp_path: Path) -> None:
         assert "compacted goals" in summary
         loaded = await memory.list_messages(new_id)
         assert any("compacted goals" in getattr(m, "content", "") for m in loaded)
+        # After compact, RAM matches DB and the persist cursor treats seed as stored.
+        assert len(state.agent.messages) == len(loaded)
+        assert state.agent.persist_from == len(state.agent.messages)
         # Old session still exists and is listable
         sessions = await memory.list_sessions(workspace=tmp_path)
         ids = {s.sid for s in sessions}
         assert old_id in ids
         assert new_id in ids
+
+        # Simulate restart: resume compact session, continue without duplicating seed.
+        state2 = ReplState(
+            config=config,
+            memory=memory,
+            workspace=tmp_path,
+            provider_name="local",
+            provider=provider,
+            model="gpt-test",
+            tools_enabled=False,
+        )
+        state2.client = SummaryClient()
+        await state2.resume_session(new_id)
+        assert len(state2.agent.messages) == len(loaded)
+        assert state2.agent.persist_from == len(state2.agent.messages)
+        assert any("compacted goals" in getattr(m, "content", "") for m in state2.agent.messages)
+        # Full original conversation still only on the old session.
+        old_loaded = await memory.list_messages(old_id)
+        assert any(isinstance(m, UserChatMessage) and m.content == "do work" for m in old_loaded)
+    finally:
+        await memory.close()
+
+
+async def test_rebuild_client_preserves_persist_cursor(tmp_path: Path) -> None:
+    _ = set_workspace_root(tmp_path)
+    memory = await MemoryStore.open(DatabaseConfig())
+    try:
+        provider = OpenAIProvider(access_key_or_token="sk-test")
+        config = ConfigStore(path=tmp_path / "plyngent.toml", document=tomlkit.document())
+        config.providers = {"local": provider}
+        state = ReplState(
+            config=config,
+            memory=memory,
+            workspace=tmp_path,
+            provider_name="local",
+            provider=provider,
+            model="gpt-test",
+            tools_enabled=False,
+        )
+        state.client = SummaryClient()
+        await state.new_session("s")
+        state.agent.replace_messages(
+            [UserChatMessage(content="hi"), AssistantChatMessage(content="yo")],
+            persisted=True,
+        )
+        assert state.agent.persist_from == 2
+        state.rebuild_client()
+        assert len(state.agent.messages) == 2
+        assert state.agent.persist_from == 2
     finally:
         await memory.close()
 

tests/test_cli/test_interrupt.py

@@ -1,16 +1,22 @@
 from __future__ import annotations
 
+import asyncio
+import signal
 from typing import TYPE_CHECKING
 
+import pytest
+
 from plyngent.cli.interrupt import (
     allow_task_cancel,
     pause_task_cancel_for_prompt,
     run_in_prompt_thread,
+    set_sigint_reinstall,
 )
 from plyngent.cli.limits import prompt_continue_limit, prompt_continue_limit_async
+from plyngent.cli.retry import run_cancellable
 
 if TYPE_CHECKING:
-    import pytest
+    pass
 
 
 def test_pause_task_cancel_for_prompt() -> None:
@@ -20,6 +26,16 @@ def test_pause_task_cancel_for_prompt() -> None:
     assert allow_task_cancel() is True
 
 
+def test_nested_pause_depth() -> None:
+    assert allow_task_cancel() is True
+    with pause_task_cancel_for_prompt():
+        assert allow_task_cancel() is False
+        with pause_task_cancel_for_prompt():
+            assert allow_task_cancel() is False
+        assert allow_task_cancel() is False
+    assert allow_task_cancel() is True
+
+
 def test_prompt_continue_limit_under_pause(monkeypatch: pytest.MonkeyPatch) -> None:
     def _confirm(*_a: object, **_k: object) -> bool:
         assert allow_task_cancel() is False
@@ -36,7 +52,6 @@ async def test_run_in_prompt_thread_pauses_cancel() -> None:
     def work() -> str:
         return "ok"
 
-    # ContextVar may not propagate to worker threads; assert pause around the call.
     result = await run_in_prompt_thread(work)
     assert result == "ok"
     assert allow_task_cancel() is True
@@ -48,3 +63,53 @@ async def test_prompt_continue_limit_async(monkeypatch: pytest.MonkeyPatch) -> N
 
     monkeypatch.setattr("click.confirm", _confirm)
     assert await prompt_continue_limit_async("too many rounds") is True
+
+
+async def test_sigint_cancels_after_prompt_pause() -> None:
+    """Regression: after a mid-turn prompt, SIGINT must still cancel the turn.
+
+    Previously, reinstalling the asyncio SIGINT handler while
+    allow_task_cancel was still False froze that value into the callback
+    forever (ContextVar snapshot at add_signal_handler).
+    """
+    loop = asyncio.get_running_loop()
+    try:
+        loop.add_signal_handler(signal.SIGINT, lambda: None)
+        loop.remove_signal_handler(signal.SIGINT)
+    except NotImplementedError, RuntimeError, ValueError:
+        pytest.skip("asyncio signal handlers not available on this platform")
+
+    started = asyncio.Event()
+    cancelled = asyncio.Event()
+
+    async def hang() -> None:
+        started.set()
+        try:
+            await asyncio.sleep(3600)
+        except asyncio.CancelledError:
+            cancelled.set()
+            raise
+
+    async def turn() -> None:
+        # Simulate soft-confirm pause mid-turn, then keep streaming.
+        with pause_task_cancel_for_prompt():
+            assert allow_task_cancel() is False
+        assert allow_task_cancel() is True
+        await hang()
+
+    task = asyncio.create_task(run_cancellable(turn()))
+    await started.wait()
+    # Give run_cancellable a tick to install the handler after the pause reinstall.
+    await asyncio.sleep(0)
+    assert allow_task_cancel() is True
+    # Deliver SIGINT the same way Ctrl+C does under asyncio.
+    loop.call_soon(lambda: None)  # ensure loop is processing
+    # Invoke the process signal: raise SIGINT to this process.
+    import os
+
+    os.kill(os.getpid(), signal.SIGINT)
+    with pytest.raises(asyncio.CancelledError):
+        await task
+    assert cancelled.is_set()
+    # Cleanup any leftover reinstall hook from run_cancellable
+    set_sigint_reinstall(None)

tests/test_cli/test_limits.py

@@ -1,6 +1,11 @@
 from __future__ import annotations
 
-from plyngent.cli.limits import install_cli_limit_hooks, prompt_confirm_tool, prompt_continue_limit
+from plyngent.cli.limits import (
+    format_tool_confirm_box,
+    install_cli_limit_hooks,
+    prompt_confirm_tool,
+    prompt_continue_limit,
+)
 from plyngent.prompting import get_prompt_backend, temporary_backend
 from plyngent.tools.process.pty_session import PtyManager
 from tests.test_prompting import ScriptedBackend
@@ -24,6 +29,17 @@ def test_prompt_confirm_tool_default_deny() -> None:
         assert prompt_confirm_tool("delete_path", {"path": "x"}, "delete path 'x'") is False
 
 
+def test_format_tool_confirm_box_multiline() -> None:
+    reason = "run_command: python3 -c (review code before allow)\nargv:\n  python3 -c print(1)\n-c code:\n  print(1)"
+    box = format_tool_confirm_box("run_command", reason)
+    assert "┌" in box and "└" in box
+    assert "confirm · tool 'run_command'" in box
+    assert "python3 -c" in box
+    assert "print(1)" in box
+    # Distinct lines, not one jammed row
+    assert box.count("\n") >= 4
+
+
 def test_install_cli_limit_hooks() -> None:
     install_cli_limit_hooks()
     assert callable(getattr(PtyManager, "_limit_continue", None))

tests/test_cli/test_readline_setup.py

@@ -183,3 +183,20 @@ def test_complete_slash_args_from_registry(tmp_path: object) -> None:
     assert complete_slash_args(state, "/help", "st") == ["status", "stream"]
     assert complete_slash_args(state, "/yolo", "") == ["on", "off", "once"]
     assert complete_slash_args(state, "/yolo", "o") == ["on", "off", "once"]
+    assert "push" in complete_slash_args(state, "/todos", "p")
+    assert "pop" in complete_slash_args(state, "/todos", "p")
+    assert "--persist" in complete_slash_args(state, "/model", "--p")
+    assert "--full" in complete_slash_args(state, "/history", "--f")
+    assert "32" in complete_slash_args(state, "/rounds", "3")
+
+    from plyngent.agent.todo_stack import TodoStack
+
+    state.todo_stack = TodoStack()
+    _ = state.todo_stack.push_group(["alpha", "beta"])
+    ids = complete_slash_args(state, "/todos", "t", prior_args=["done"])
+    assert "t1" in ids
+    assert "t2" in ids
+
+    state.remember_session_ids([3, 12, 40])
+    assert complete_slash_args(state, "/resume", "1") == ["12"]
+    assert complete_slash_args(state, "/delete", "4") == ["40"]

tests/test_cli/test_repl_commands.py

@@ -109,8 +109,10 @@ async def test_help_command_usage_line(state: ReplState, capsys: pytest.CaptureF
 async def test_help_history_no_fake_options(state: ReplState, capsys: pytest.CaptureFixture[str]) -> None:
     assert await handle_slash(state, "/help history") is True
     out = capsys.readouterr().out
-    assert "Usage: /history [N]" in out
-    assert "Options:" not in out
+    assert "Usage: /history" in out
+    # Real flags for full/preview are documented; Click's meta --help is not.
+    assert "--full" in out
+    assert "--preview" in out
     assert "  --help" not in out
 
 
@@ -341,6 +343,36 @@ async def test_verbose_toggle(state: ReplState) -> None:
     assert get_verbose_tool_results() is False
 
 
+async def test_model_persist_writes_config(
+    state: ReplState, tmp_path: Path, capsys: pytest.CaptureFixture[str]
+) -> None:
+    # Seed a TOML-backed store so write() has a real path.
+    path = tmp_path / "plyngent.toml"
+    _ = path.write_text(
+        """
+[providers.local]
+preset = "openai"
+access_key_or_token = "sk-test"
+
+[providers.local.models.gpt-test]
+""",
+        encoding="utf-8",
+    )
+    from plyngent.config import load as load_config
+
+    state.config = load_config(path)
+    state.provider_name = "local"
+    state.provider = state.config.providers["local"]
+    state.model = "gpt-new-id"
+    assert await handle_slash(state, "/model --persist") is True
+    out = capsys.readouterr().out
+    assert "persisted model" in out
+    assert "gpt-new-id" in out
+    state.config.reload()
+    assert "gpt-new-id" in state.config.providers["local"].models
+    assert "gpt-test" in state.config.providers["local"].models
+
+
 async def test_yolo_toggle(state: ReplState, capsys: pytest.CaptureFixture[str]) -> None:
     assert state.effective_yolo() == "off"
     assert state.soft_confirm_enabled() is True
@@ -414,10 +446,61 @@ async def test_history(state: ReplState, capsys: pytest.CaptureFixture[str]) ->
     ]
     assert await handle_slash(state, "/history") is True
     out = capsys.readouterr().out
+    assert "mode=preview" in out
     assert "user: hello" in out
     assert "assistant: hi there" in out
 
 
+async def test_history_last_full(state: ReplState, capsys: pytest.CaptureFixture[str]) -> None:
+    from plyngent.lmproto.openai_compatible.model import AssistantChatMessage, UserChatMessage
+
+    long_body = "# Title\n\n" + ("paragraph text. " * 20)
+    state.agent.messages = [
+        UserChatMessage(content="hello"),
+        AssistantChatMessage(content=long_body),
+    ]
+    assert await handle_slash(state, "/history last") is True
+    out = capsys.readouterr().out
+    assert "mode=full" in out
+    assert "assistant:" in out
+    # Full mode should not use the 200-char preview ellipsis on the body alone
+    assert long_body[:50] in out or "Title" in out
+
+
+async def test_history_one_full(state: ReplState, capsys: pytest.CaptureFixture[str]) -> None:
+    from plyngent.lmproto.openai_compatible.model import UserChatMessage
+
+    state.agent.messages = [UserChatMessage(content="only me")]
+    assert await handle_slash(state, "/history 1") is True
+    out = capsys.readouterr().out
+    assert "mode=full" in out
+    assert "only me" in out
+
+
+async def test_history_one_preview_flag(state: ReplState, capsys: pytest.CaptureFixture[str]) -> None:
+    from plyngent.lmproto.openai_compatible.model import UserChatMessage
+
+    state.agent.messages = [UserChatMessage(content="x" * 250)]
+    assert await handle_slash(state, "/history 1 --preview") is True
+    out = capsys.readouterr().out
+    assert "mode=preview" in out
+    assert "…" in out
+
+
+async def test_history_full_flag(state: ReplState, capsys: pytest.CaptureFixture[str]) -> None:
+    from plyngent.lmproto.openai_compatible.model import AssistantChatMessage, UserChatMessage
+
+    body = "full " * 100
+    state.agent.messages = [
+        UserChatMessage(content="u"),
+        AssistantChatMessage(content=body),
+    ]
+    assert await handle_slash(state, "/history 2 --full") is True
+    out = capsys.readouterr().out
+    assert "mode=full" in out
+    assert body[:40] in out
+
+
 async def test_rounds(state: ReplState) -> None:
     assert await handle_slash(state, "/rounds 40") is True
     assert state.max_rounds == 40

tests/test_config/test_config.py

@@ -179,6 +179,39 @@ def test_write_new_config() -> None:
     assert config.providers["foo2"].access_key_or_token == "sk-00301212"
 
 
+def test_ensure_model_and_merge_models(tmp_path: Path) -> None:
+    path = tmp_path / "models-persist.toml"
+    _ = path.write_text(
+        """
+[providers.local]
+preset = "openai-compatible"
+access_key_or_token = "sk-test"
+url = "https://example/v1"
+
+[providers.local.models.base]
+""",
+        encoding="utf-8",
+    )
+    config = plyngent.config.load(path)
+    assert "base" in config.providers["local"].models
+    assert "extra" not in config.providers["local"].models
+
+    provider = config.ensure_model("local", "extra")
+    assert "extra" in provider.models
+    assert "base" in provider.models
+    # idempotent
+    _ = config.ensure_model("local", "extra")
+    config.write()
+    config.reload()
+    assert set(config.providers["local"].models) == {"base", "extra"}
+    assert config.providers["local"].access_key_or_token == "sk-test"
+
+    _ = config.merge_models("local", ["extra", "remote-a", "remote-b"])
+    config.write()
+    config.reload()
+    assert set(config.providers["local"].models) == {"base", "extra", "remote-a", "remote-b"}
+
+
 def test_update_config() -> None:
     file = Path(__file__).parent / "plyngent-edit-2.toml"
     _ = shutil.copy(Path(__file__).parent / "plyngent-valid.toml", file)

tests/test_tools/conftest.py

@@ -4,7 +4,11 @@ from typing import TYPE_CHECKING
 
 import pytest
 
-from plyngent.tools.workspace import clear_workspace_root, set_workspace_root
+from plyngent.tools.workspace import (
+    clear_workspace_allowlist,
+    clear_workspace_root,
+    set_workspace_root,
+)
 
 if TYPE_CHECKING:
     from collections.abc import Iterator
@@ -14,6 +18,8 @@ if TYPE_CHECKING:
 @pytest.fixture
 def workspace(tmp_path: Path) -> Iterator[Path]:
     clear_workspace_root()
+    clear_workspace_allowlist()
     root = set_workspace_root(tmp_path)
     yield root
+    clear_workspace_allowlist()
     clear_workspace_root()

tests/test_tools/test_danger.py

@@ -11,18 +11,71 @@ def test_classify_delete_and_move() -> None:
     assert "move" in (classify_danger("move_path", {"src": "a", "dst": "b"}) or "")
 
 
-def test_classify_copy_overwrite_only() -> None:
-    assert classify_danger("copy_path", {"src": "a", "dst": "b"}) is None
-    assert "overwrite" in (classify_danger("copy_path", {"src": "a", "dst": "b", "overwrite": True}) or "")
+def test_classify_copy() -> None:
+    assert "copy" in (classify_danger("copy_path", {"src": "a", "dst": "b"}) or "")
 
 
-def test_classify_write_file_overwrite(workspace: object) -> None:
-    assert isinstance(workspace, Path)
-    _ = (workspace / "x.txt").write_text("old", encoding="utf-8")
-    assert "overwrite" in (classify_danger("write_file", {"path": "x.txt", "content": "n"}) or "")
-    assert classify_danger("write_file", {"path": "new.txt", "content": "n"}) is None
+def test_classify_write_and_edits(tmp_path: Path) -> None:
+    from plyngent.tools.workspace import clear_workspace_root, set_workspace_root
+
+    set_workspace_root(tmp_path)
+    try:
+        reason = classify_danger("write_file", {"path": "x.txt"})
+        assert reason is not None and "write file" in reason
+        assert "edit" in (classify_danger("edit_replace", {"path": "x.txt"}) or "")
+        assert "lines" in (classify_danger("edit_lineno", {"path": "x.txt", "start_line": 1, "end_line": 2}) or "")
+    finally:
+        clear_workspace_root()
 
 
 def test_classify_safe_tools() -> None:
     assert classify_danger("read_file", {"path": "a"}) is None
+    assert classify_danger("listdir", {"path": "."}) is None
     assert classify_danger("run_command", {"command": ["echo", "hi"]}) is None
+    assert classify_danger("open_pty", {"command": ["true"]}) is None
+    assert classify_danger("run_command", {"command": ["ls", "-la"]}) is None
+
+
+def test_classify_shell_and_dash_c() -> None:
+    r = classify_danger("run_command", {"command": ["bash", "-c", "rm -rf /"]})
+    assert r is not None
+    assert "bash -c" in r
+    assert "rm -rf" in r
+
+    r2 = classify_danger("run_command", {"command": ["python3", "-c", "print(1)"]})
+    assert r2 is not None
+    assert "python" in r2
+    assert "-c" in r2
+    assert "print(1)" in r2
+
+    r_py = classify_danger("run_command", {"command": ["python", "-c", "import os"]})
+    assert r_py is not None and "python -c" in r_py
+
+    r3 = classify_danger("open_pty", {"command": ["bash"]})
+    assert r3 is not None and "bash" in r3
+    assert "interactive" in r3 or "review" in r3
+
+    r4 = classify_danger("open_pty", {"command": ["python3"]})
+    assert r4 is not None and "python" in r4
+
+    r5 = classify_danger("open_pty", {"command": ["python3", "-c", "x=1"]})
+    assert r5 is not None and "-c" in r5
+
+
+async def test_confirm_deny_with_comment() -> None:
+    from plyngent.agent.tools import ToolRegistry, tool
+    from plyngent.tools.danger import classify_danger as danger
+
+    @tool
+    def delete_path(path: str) -> str:
+        return f"deleted {path}"
+
+    async def deny_comment(name: str, args: object, reason: str) -> str:
+        del name, args, reason
+        return "too destructive for this session"
+
+    reg = ToolRegistry([delete_path], danger=danger, on_confirm=deny_comment)
+    out = await reg.execute("delete_path", '{"path": "x"}')
+    assert "denied" in out
+    assert "user comment:" in out
+    assert "too destructive" in out

tests/test_tools/test_file.py

@@ -35,6 +35,18 @@ def test_read_offset_limit(workspace: object) -> None:
     assert call_sync(read_file, "lines.txt", offset=1, limit=2) == "b\nc\n"
 
 
+def test_read_with_lineno(workspace: object) -> None:
+    del workspace
+    _ = call_sync(write_file, "num.txt", "a\nb\nc\n")
+    out = call_sync(read_file, "num.txt", with_lineno=True)
+    assert "     1|a\n" in out
+    assert "     2|b\n" in out
+    assert "     3|c\n" in out
+    # offset is 0-based; line numbers stay absolute 1-based file lines
+    mid = call_sync(read_file, "num.txt", offset=1, limit=1, with_lineno=True)
+    assert mid == "     2|b\n"
+
+
 def test_listdir_missing(workspace: object) -> None:
     del workspace
     assert "error" in call_sync(listdir, "nope")

tests/test_tools/test_process.py

@@ -4,7 +4,14 @@ import asyncio
 import sys
 from pathlib import Path
 
-from plyngent.tools.process import close_pty, open_pty, read_pty, run_command, write_pty
+from plyngent.tools.process import (
+    close_pty,
+    open_pty,
+    read_pty,
+    run_command,
+    write_pty,
+    write_pty_keys,
+)
 from plyngent.tools.process.pty_session import PtyManager
 from plyngent.tools.workspace import set_command_denylist
 from tests.test_tools.helpers import call_async, call_sync
@@ -289,6 +296,85 @@ def test_pty_master_not_inheritable(workspace: object) -> None:
         PtyManager.close_all()
 
 
+def test_decode_write_data_escapes() -> None:
+    from plyngent.tools.process.pty_terminal import decode_write_data
+
+    assert decode_write_data(r"\x0f") == "\x0f"
+    assert decode_write_data("ctrl+x") == "\x18"
+    assert decode_write_data("CTRL+O") == "\x0f"
+    assert decode_write_data(r"\e") == "\x1b"
+    assert decode_write_data("key=esc") == "\x1b"
+    assert decode_write_data("key=enter") == "\r"
+    assert decode_write_data(r"a\nb") == "a\nb"
+    assert decode_write_data("plain") == "plain"
+
+
+def test_sanitize_pty_output_escapes_csi() -> None:
+    from plyngent.tools.process.pty_terminal import sanitize_pty_output_for_tool
+
+    raw = chr(0x1B) + "[?1049hhello" + chr(0x1B) + "[0m" + chr(7)
+    safe = sanitize_pty_output_for_tool(raw)
+    assert chr(0x1B) not in safe
+    assert "\\x1b" in safe
+    assert "hello" in safe
+    assert "\\x07" in safe
+
+
+def test_close_all_empty_is_noop() -> None:
+    """Ctrl-D / chat exit with no sessions must not touch the host TTY."""
+    PtyManager.close_all()
+
+
+async def test_read_pty_sanitizes_esc(workspace: object) -> None:
+    del workspace
+    try:
+        opened = call_sync(open_pty, _py("print(chr(0x1B)+'[31mred'+chr(0x1B)+'[0m')"))
+        session_id = _session_id(opened)
+        text = await call_async(read_pty, session_id, timeout=2.0, until="red")
+        assert "red" in text
+        payload = text.split("--- data ---", 1)[-1]
+        assert chr(0x1B) not in payload
+        assert "\\x1b" in payload or "red" in payload
+        _ = await call_async(close_pty, session_id)
+    finally:
+        PtyManager.close_all()
+
+
+async def test_write_pty_keys_ctrl_escape(workspace: object) -> None:
+    del workspace
+    try:
+        opened = call_sync(
+            open_pty,
+            _py(
+                "import sys\n"
+                "data = sys.stdin.buffer.read(1)\n"
+                "sys.stdout.buffer.write(data)\n"
+                "sys.stdout.buffer.flush()\n"
+            ),
+        )
+        session_id = _session_id(opened)
+        written = call_sync(write_pty_keys, session_id, "ctrl+c")
+        assert "wrote=1" in written
+        text = await call_async(read_pty, session_id, timeout=2.0)
+        assert "error" not in text.lower() or "alive=" in text
+        _ = await call_async(close_pty, session_id)
+    finally:
+        PtyManager.close_all()
+
+
+def test_write_pty_is_literal() -> None:
+    """Plain write_pty must not call the keys decoder."""
+    import inspect
+
+    from plyngent.tools.process.pty_terminal import decode_write_data
+
+    assert decode_write_data("press ctrl+c to cancel") == "press " + chr(3) + " to cancel"
+    src = inspect.getsource(write_pty.handler)
+    assert "decode_write_data" not in src
+    doc = write_pty.description or write_pty.handler.__doc__ or ""
+    assert "literal" in doc.lower()
+
+
 def test_pty_backend_available() -> None:
     from plyngent.tools.process.pty_backend import pty_available
 

tests/test_tools/test_temp_workspace.py

@@ -0,0 +1,64 @@
+from __future__ import annotations
+
+from pathlib import Path
+
+import pytest
+
+from plyngent.tools.file import read_file, write_file
+from plyngent.tools.temp_workspace import cleanup_temporary_workspaces, new_temporary_workspace
+from plyngent.tools.workspace import (
+    WorkspaceError,
+    clear_workspace_allowlist,
+    list_workspace_allowlist,
+    resolve_path,
+)
+from tests.test_tools.helpers import call_sync
+
+
+def _temp_path_from_tool_output(out: str) -> Path:
+    line = next(part for part in out.splitlines() if part.startswith("temporary_workspace="))
+    return Path(line.split("=", 1)[1].strip())
+
+
+def test_new_temporary_workspace_allowlist(workspace: object) -> None:
+    assert isinstance(workspace, Path)
+    out = call_sync(new_temporary_workspace, "unit")
+    assert "temporary_workspace=" in out
+    assert "project workspace unchanged" in out
+    temp = _temp_path_from_tool_output(out)
+    assert temp.is_dir()
+    assert temp in list_workspace_allowlist()
+
+    # Absolute path under temp is allowed; project relative still works.
+    target = temp / "scratch.txt"
+    _ = target.write_text("hello-temp", encoding="utf-8")
+    assert resolve_path(str(target)) == target.resolve()
+    assert call_sync(read_file, str(target)) == "hello-temp"
+
+    _ = call_sync(write_file, "project.txt", "proj")
+    assert call_sync(read_file, "project.txt") == "proj"
+
+    # Sibling under system temp that we did not allowlist still fails.
+    outside = temp.parent / "not-ours-should-fail"
+    with pytest.raises(WorkspaceError, match="escapes"):
+        _ = resolve_path(str(outside))
+
+
+def test_cleanup_removes_owned_temps(workspace: object) -> None:
+    assert isinstance(workspace, Path)
+    out = call_sync(new_temporary_workspace)
+    temp = _temp_path_from_tool_output(out)
+    assert temp.is_dir()
+    n = cleanup_temporary_workspaces()
+    assert n >= 1
+    assert not temp.exists()
+    assert list_workspace_allowlist() == []
+
+
+def test_prefix_sanitized(workspace: object) -> None:
+    del workspace
+    out = call_sync(new_temporary_workspace, "bad/../x y!")
+    assert "temporary_workspace=" in out
+    assert not out.startswith("error")
+    _ = cleanup_temporary_workspaces()
+    clear_workspace_allowlist()

tests/test_tools/test_tree.py

@@ -83,3 +83,58 @@ def test_tree_invalid_limits(workspace: object) -> None:
     del workspace
     assert "max_depth" in call_sync(tree, ".", max_depth=0)
     assert "max_entries" in call_sync(tree, ".", max_entries=0)
+
+
+def test_tree_default_noise_dirs(workspace: object) -> None:
+    assert isinstance(workspace, Path)
+    (workspace / "src").mkdir()
+    _ = (workspace / "src" / "app.py").write_text("x", encoding="utf-8")
+    (workspace / "node_modules").mkdir()
+    _ = (workspace / "node_modules" / "pkg.js").write_text("x", encoding="utf-8")
+    (workspace / "__pycache__").mkdir()
+    _ = (workspace / "__pycache__" / "x.pyc").write_text("x", encoding="utf-8")
+    out = call_sync(tree, ".")
+    assert "src/" in out
+    assert "app.py" in out
+    assert "node_modules" not in out
+    assert "__pycache__" not in out
+
+
+def test_tree_skip_dirs_empty_shows_noise(workspace: object) -> None:
+    assert isinstance(workspace, Path)
+    (workspace / "node_modules").mkdir()
+    _ = (workspace / "node_modules" / "pkg.js").write_text("x", encoding="utf-8")
+    out = call_sync(tree, ".", skip_dirs=[])
+    assert "node_modules/" in out
+    assert "pkg.js" in out
+
+
+def test_tree_skip_dirs_custom(workspace: object) -> None:
+    assert isinstance(workspace, Path)
+    (workspace / "keep_me").mkdir()
+    _ = (workspace / "keep_me" / "a.txt").write_text("x", encoding="utf-8")
+    (workspace / "drop_me").mkdir()
+    _ = (workspace / "drop_me" / "b.txt").write_text("x", encoding="utf-8")
+    # Custom list replaces default noise set (node_modules not in list → would show if present).
+    out = call_sync(tree, ".", skip_dirs=["drop_me"])
+    assert "keep_me/" in out
+    assert "drop_me" not in out
+
+
+def test_tree_path_denylist_walk(workspace: object) -> None:
+    from plyngent.tools.workspace import set_path_denylist
+
+    assert isinstance(workspace, Path)
+    (workspace / "ok").mkdir()
+    _ = (workspace / "ok" / "a.txt").write_text("x", encoding="utf-8")
+    (workspace / "secrets").mkdir()
+    _ = (workspace / "secrets" / "key.txt").write_text("x", encoding="utf-8")
+    set_path_denylist(["/secrets"])
+    try:
+        out = call_sync(tree, ".")
+        assert "ok/" in out
+        assert "secrets" not in out
+        out2 = call_sync(tree, ".", apply_path_denylist=False, skip_dirs=[])
+        assert "secrets/" in out2
+    finally:
+        set_path_denylist(None)