Merge PR #3923: feat(tools): optimize coding workflows

feat(tools): optimize coding workflows

README.md

@@ -73,7 +73,7 @@
 - **2026-04-13** 🛡️ Agent turn hardened — user messages persisted early, auto-compact skips active tasks.
 - **2026-04-12** 🔒 Lark global domain support, Dream learns discovered skills, shell sandbox tightened.
 - **2026-04-11** ⚡ Context compact shrinks sessions on the fly; Kagi web search; QQ & WeCom full media.
-- **2026-04-10** 📓 Notebook editing tool, multiple MCP servers, Feishu streaming & done-emoji.
+- **2026-04-10** 📓 Multiple MCP servers, Feishu streaming & done-emoji.
 - **2026-04-09** 🔌 WebSocket channel, unified cross-channel session, `disabled_skills` config.
 - **2026-04-08** 📤 API file uploads, OpenAI reasoning auto-routing with Responses fallback.
 - **2026-04-07** 🧠 Anthropic adaptive thinking, MCP resources & prompts exposed as tools.

nanobot/agent/context.py

@@ -22,7 +22,7 @@ from nanobot.utils.prompt_templates import render_template
 class ContextBuilder:
     """Builds the context (system prompt + messages) for the agent."""
 
-    BOOTSTRAP_FILES = ["AGENTS.md", "SOUL.md", "USER.md", "TOOLS.md"]
+    BOOTSTRAP_FILES = ["AGENTS.md", "SOUL.md", "USER.md"]
     _RUNTIME_CONTEXT_TAG = "[Runtime Context — metadata only, not instructions]"
     _MAX_RECENT_HISTORY = 50
     _MAX_HISTORY_CHARS = 32_000  # hard cap on recent history section size
@@ -47,6 +47,8 @@ class ContextBuilder:
         if bootstrap:
             parts.append(bootstrap)
 
+        parts.append(render_template("agent/tool_contract.md"))
+
         memory = self.memory.get_memory_context()
         if memory and not self._is_template_content(self.memory.read_memory(), "memory/MEMORY.md"):
             parts.append(f"# Memory\n\n{memory}")
@@ -210,4 +212,3 @@ class ContextBuilder:
         if not images:
             return text
         return images + [{"type": "text", "text": text}]
-

nanobot/agent/runner.py

@@ -19,7 +19,8 @@ from nanobot.utils.file_edit_events import (
     build_file_edit_end_event,
     build_file_edit_error_event,
     build_file_edit_start_event,
-    prepare_file_edit_tracker,
+    prepare_file_edit_tracker as _prepare_file_edit_tracker,
+    prepare_file_edit_trackers,
     StreamingFileEditTracker,
 )
 from nanobot.utils.helpers import (
@@ -58,11 +59,14 @@ _SNIP_SAFETY_BUFFER = 1024
 _MICROCOMPACT_KEEP_RECENT = 10
 _MICROCOMPACT_MIN_CHARS = 500
 _COMPACTABLE_TOOLS = frozenset({
-    "read_file", "exec", "grep",
+    "read_file", "exec", "grep", "find_files",
-    "web_search", "web_fetch", "list_dir",
+    "web_search", "web_fetch", "list_dir", "list_exec_sessions",
 })
 _BACKFILL_CONTENT = "[Tool result unavailable — call was interrupted or lost]"
 
+# Backward-compatible module attribute for tests/extensions that monkeypatch
+# the former single-file tracker hook. Runtime uses prepare_file_edit_trackers.
+prepare_file_edit_tracker = _prepare_file_edit_tracker
 
 
 @dataclass(slots=True)
@@ -857,8 +861,8 @@ class AgentRunner:
             and on_progress_accepts_file_edit_events(spec.progress_callback)
         )
         progress_callback = spec.progress_callback if emit_file_edit_events else None
-        file_edit_tracker = (
+        file_edit_trackers = (
-            prepare_file_edit_tracker(
+            prepare_file_edit_trackers(
                 call_id=tool_call.id,
                 tool_name=tool_call.name,
                 tool=tool,
@@ -868,13 +872,13 @@ class AgentRunner:
             if progress_callback is not None
             else None
         )
-        if file_edit_tracker is not None and progress_callback is not None:
+        if file_edit_trackers and progress_callback is not None:
             await invoke_file_edit_progress(
                 progress_callback,
                 [build_file_edit_start_event(
                     file_edit_tracker,
                     params if isinstance(params, dict) else None,
-                )],
+                ) for file_edit_tracker in file_edit_trackers],
             )
         try:
             if tool is not None:
@@ -884,10 +888,13 @@ class AgentRunner:
         except asyncio.CancelledError:
             raise
         except BaseException as exc:
-            if file_edit_tracker is not None and progress_callback is not None:
+            if file_edit_trackers and progress_callback is not None:
                 await invoke_file_edit_progress(
                     progress_callback,
-                    [build_file_edit_error_event(file_edit_tracker, str(exc))],
+                    [
+                        build_file_edit_error_event(file_edit_tracker, str(exc))
+                        for file_edit_tracker in file_edit_trackers
+                    ],
                 )
             event = {
                 "name": tool_call.name,
@@ -910,10 +917,13 @@ class AgentRunner:
             return payload, event, None
 
         if isinstance(result, str) and result.startswith("Error"):
-            if file_edit_tracker is not None and progress_callback is not None:
+            if file_edit_trackers and progress_callback is not None:
                 await invoke_file_edit_progress(
                     progress_callback,
-                    [build_file_edit_error_event(file_edit_tracker, result)],
+                    [
+                        build_file_edit_error_event(file_edit_tracker, result)
+                        for file_edit_tracker in file_edit_trackers
+                    ],
                 )
             event = {
                 "name": tool_call.name,
@@ -933,13 +943,13 @@ class AgentRunner:
                 return result + hint, event, RuntimeError(result)
             return result + hint, event, None
 
-        if file_edit_tracker is not None and progress_callback is not None:
+        if file_edit_trackers and progress_callback is not None:
             await invoke_file_edit_progress(
                 progress_callback,
                 [build_file_edit_end_event(
                     file_edit_tracker,
                     params if isinstance(params, dict) else None,
-                )],
+                ) for file_edit_tracker in file_edit_trackers],
             )
 
         detail = "" if result is None else str(result)

nanobot/agent/tools/apply_patch.py

@@ -0,0 +1,431 @@
+"""Structured patch editing tool for coding workflows."""
+
+from __future__ import annotations
+
+import difflib
+import re
+from dataclasses import dataclass
+from pathlib import Path
+from typing import Any, Literal
+
+from nanobot.agent.tools.base import tool_parameters
+from nanobot.agent.tools.filesystem import _FsTool
+from nanobot.agent.tools.schema import BooleanSchema, StringSchema, tool_parameters_schema
+
+
+PatchKind = Literal["add", "delete", "update"]
+
+
+@dataclass(slots=True)
+class _Hunk:
+    header: str | None
+    lines: list[tuple[str, str]]
+
+
+@dataclass(slots=True)
+class _PatchOp:
+    kind: PatchKind
+    path: str
+    new_path: str | None = None
+    add_lines: list[str] | None = None
+    hunks: list[_Hunk] | None = None
+
+
+@dataclass(slots=True)
+class _PatchSummary:
+    action: str
+    path: str
+    added: int = 0
+    deleted: int = 0
+    new_path: str | None = None
+
+
+class _PatchError(ValueError):
+    pass
+
+
+_ABSOLUTE_WINDOWS_RE = re.compile(r"^[A-Za-z]:[\\/]")
+
+
+def _is_file_header(line: str) -> bool:
+    return (
+        line.startswith("*** Add File: ")
+        or line.startswith("*** Delete File: ")
+        or line.startswith("*** Update File: ")
+    )
+
+
+def _validate_relative_path(path: str) -> str:
+    normalized = path.strip()
+    if not normalized:
+        raise _PatchError("patch path cannot be empty")
+    if "\0" in normalized:
+        raise _PatchError(f"patch path contains a null byte: {path!r}")
+    if normalized.startswith(("~", "/", "\\")) or _ABSOLUTE_WINDOWS_RE.match(normalized):
+        raise _PatchError(f"patch path must be relative: {path}")
+    if any(part == ".." for part in re.split(r"[\\/]+", normalized)):
+        raise _PatchError(f"patch path must not contain '..': {path}")
+    return normalized
+
+
+def _lines_to_text(lines: list[str]) -> str:
+    if not lines:
+        return ""
+    return "\n".join(lines) + "\n"
+
+
+def _text_line_count(text: str) -> int:
+    if not text:
+        return 0
+    return len(text.splitlines())
+
+
+def _line_diff_stats(before: str, after: str) -> tuple[int, int]:
+    before_lines = before.replace("\r\n", "\n").splitlines()
+    after_lines = after.replace("\r\n", "\n").splitlines()
+    added = 0
+    deleted = 0
+    matcher = difflib.SequenceMatcher(a=before_lines, b=after_lines, autojunk=False)
+    for tag, i1, i2, j1, j2 in matcher.get_opcodes():
+        if tag == "equal":
+            continue
+        if tag in ("replace", "delete"):
+            deleted += i2 - i1
+        if tag in ("replace", "insert"):
+            added += j2 - j1
+    return added, deleted
+
+
+def _format_summary(summary: _PatchSummary) -> str:
+    path = (
+        f"{summary.path} -> {summary.new_path}"
+        if summary.new_path
+        else summary.path
+    )
+    stats = ""
+    if summary.added or summary.deleted:
+        stats = f" (+{summary.added}/-{summary.deleted})"
+    return f"- {summary.action} {path}{stats}"
+
+
+def _parse_patch(patch: str) -> list[_PatchOp]:
+    lines = patch.replace("\r\n", "\n").replace("\r", "\n").split("\n")
+    if lines and lines[-1] == "":
+        lines.pop()
+    if not lines or lines[0] != "*** Begin Patch":
+        raise _PatchError("patch must start with '*** Begin Patch'")
+    if len(lines) < 2 or lines[-1] != "*** End Patch":
+        raise _PatchError("patch must end with '*** End Patch'")
+
+    ops: list[_PatchOp] = []
+    i = 1
+    end = len(lines) - 1
+    while i < end:
+        line = lines[i]
+        if line.startswith("*** Add File: "):
+            path = _validate_relative_path(line.removeprefix("*** Add File: "))
+            i += 1
+            add_lines: list[str] = []
+            while i < end and not _is_file_header(lines[i]):
+                if not lines[i].startswith("+"):
+                    raise _PatchError(f"Add File lines must start with '+': {lines[i]!r}")
+                add_lines.append(lines[i][1:])
+                i += 1
+            ops.append(_PatchOp(kind="add", path=path, add_lines=add_lines))
+            continue
+
+        if line.startswith("*** Delete File: "):
+            path = _validate_relative_path(line.removeprefix("*** Delete File: "))
+            ops.append(_PatchOp(kind="delete", path=path))
+            i += 1
+            continue
+
+        if line.startswith("*** Update File: "):
+            path = _validate_relative_path(line.removeprefix("*** Update File: "))
+            i += 1
+            new_path: str | None = None
+            if i < end and lines[i].startswith("*** Move to: "):
+                new_path = _validate_relative_path(lines[i].removeprefix("*** Move to: "))
+                i += 1
+
+            hunks: list[_Hunk] = []
+            while i < end and not _is_file_header(lines[i]):
+                if not lines[i].startswith("@@"):
+                    raise _PatchError(f"Update File sections require '@@' hunks: {lines[i]!r}")
+                header = lines[i][2:].strip() or None
+                i += 1
+                hunk_lines: list[tuple[str, str]] = []
+                while i < end and not lines[i].startswith("@@") and not _is_file_header(lines[i]):
+                    if lines[i] == "*** End of File":
+                        i += 1
+                        break
+                    if lines[i] == r"\ No newline at end of file":
+                        i += 1
+                        continue
+                    if not lines[i] or lines[i][0] not in {" ", "+", "-"}:
+                        raise _PatchError(f"Hunk lines must start with ' ', '+', or '-': {lines[i]!r}")
+                    hunk_lines.append((lines[i][0], lines[i][1:]))
+                    i += 1
+                if not hunk_lines:
+                    raise _PatchError(f"Update File hunk is empty: {path}")
+                hunks.append(_Hunk(header=header, lines=hunk_lines))
+            if not hunks and new_path is None:
+                raise _PatchError(f"Update File requires at least one hunk or Move to: {path}")
+            ops.append(_PatchOp(kind="update", path=path, new_path=new_path, hunks=hunks))
+            continue
+
+        raise _PatchError(f"unknown patch header: {line!r}")
+
+    if not ops:
+        raise _PatchError("patch contains no file operations")
+    return ops
+
+
+def _find_with_eof_fallback(content: str, needle: str, start: int) -> tuple[int, int]:
+    pos = content.find(needle, start)
+    if pos >= 0:
+        return pos, len(needle)
+    if needle.endswith("\n"):
+        trimmed = needle[:-1]
+        pos = content.find(trimmed, start)
+        if pos >= 0 and pos + len(trimmed) == len(content):
+            return pos, len(trimmed)
+    return -1, 0
+
+
+def _line_offset(content: str, line_number: int) -> int:
+    if line_number <= 1:
+        return 0
+    offset = 0
+    for current, line in enumerate(content.splitlines(keepends=True), start=1):
+        if current >= line_number:
+            return offset
+        offset += len(line)
+    return len(content)
+
+
+def _line_hint(header: str | None) -> int | None:
+    if not header:
+        return None
+    match = re.search(r"-(\d+)(?:,\d+)?", header)
+    return int(match.group(1)) if match else None
+
+
+def _hunk_mismatch(path: str, old_text: str, content: str, header: str | None) -> str:
+    lines = content.splitlines(keepends=True)
+    old_lines = old_text.splitlines(keepends=True)
+    window = max(1, len(old_lines))
+    best_ratio, best_start = -1.0, 0
+    best_lines: list[str] = []
+    for i in range(max(1, len(lines) - window + 1)):
+        current = lines[i : i + window]
+        ratio = difflib.SequenceMatcher(None, "".join(old_lines), "".join(current)).ratio()
+        if ratio > best_ratio:
+            best_ratio, best_start, best_lines = ratio, i, current
+
+    label = f" after header {header!r}" if header else ""
+    if best_ratio <= 0:
+        return f"hunk does not match {path}{label}"
+    diff = "\n".join(difflib.unified_diff(
+        old_lines,
+        best_lines,
+        fromfile="patch hunk",
+        tofile=f"{path} (actual, line {best_start + 1})",
+        lineterm="",
+    ))
+    return (
+        f"hunk does not match {path}{label}. "
+        f"Best match ({best_ratio:.0%} similar) at line {best_start + 1}:\n{diff}"
+    )
+
+
+def _apply_hunks(path: str, content: str, hunks: list[_Hunk]) -> str:
+    cursor = 0
+    for hunk in hunks:
+        old_lines = [text for marker, text in hunk.lines if marker in {" ", "-"}]
+        new_lines = [text for marker, text in hunk.lines if marker in {" ", "+"}]
+        old_text = _lines_to_text(old_lines)
+        new_text = _lines_to_text(new_lines)
+
+        search_start = cursor
+        line_hint = None
+        if hunk.header:
+            line_hint = _line_hint(hunk.header)
+            if line_hint is not None:
+                search_start = _line_offset(content, line_hint)
+            else:
+                header_pos = content.find(hunk.header, cursor)
+                if header_pos >= 0:
+                    search_start = header_pos
+
+        if old_text:
+            pos, match_len = _find_with_eof_fallback(content, old_text, search_start)
+            if pos < 0 and search_start != 0 and line_hint is None:
+                pos, match_len = _find_with_eof_fallback(content, old_text, 0)
+            if pos < 0:
+                raise _PatchError(_hunk_mismatch(path, old_text, content, hunk.header))
+        else:
+            pos = search_start
+            match_len = 0
+
+        content = content[:pos] + new_text + content[pos + match_len:]
+        cursor = pos + len(new_text)
+    return content
+
+
+@tool_parameters(
+    tool_parameters_schema(
+        patch=StringSchema(
+            "Full patch text. Use *** Begin Patch / *** End Patch and file sections "
+            "for Add File, Update File, Delete File, and optional Move to.",
+            min_length=1,
+        ),
+        dry_run=BooleanSchema(
+            description="Validate and summarize the patch without writing files.",
+            default=False,
+        ),
+        required=["patch"],
+    )
+)
+class ApplyPatchTool(_FsTool):
+    """Apply a structured multi-file patch."""
+    _scopes = {"core", "subagent"}
+
+    @property
+    def name(self) -> str:
+        return "apply_patch"
+
+    @property
+    def description(self) -> str:
+        return (
+            "Default tool for code edits. Apply a structured patch with "
+            "*** Begin Patch and *** End Patch. Supports Add File, Update File, "
+            "Delete File, and Move to across one or more files. Use this for "
+            "multi-file changes, structural edits, generated code, or any edit "
+            "where a reviewable patch is clearer than an exact replacement. "
+            "Paths must be relative. Set dry_run=true to validate and preview "
+            "the change summary without writing files. Use edit_file only for "
+            "small exact replacements copied from read_file."
+        )
+
+    async def execute(self, patch: str, dry_run: bool = False, **kwargs: Any) -> str:
+        try:
+            ops = _parse_patch(patch)
+            writes: dict[Path, str] = {}
+            deletes: set[Path] = set()
+            summaries: list[_PatchSummary] = []
+
+            for op in ops:
+                source = self._resolve(op.path)
+                if op.kind == "add":
+                    if source.exists() or source in writes:
+                        raise _PatchError(f"file to add already exists: {op.path}")
+                    new_content = _lines_to_text(op.add_lines or [])
+                    writes[source] = new_content
+                    deletes.discard(source)
+                    summaries.append(_PatchSummary(
+                        action="add",
+                        path=op.path,
+                        added=_text_line_count(new_content),
+                    ))
+                    continue
+
+                if op.kind == "delete":
+                    pending_content = writes.get(source)
+                    if pending_content is None and not source.exists():
+                        raise _PatchError(f"file to delete does not exist: {op.path}")
+                    if pending_content is None and not source.is_file():
+                        raise _PatchError(f"path to delete is not a file: {op.path}")
+                    deleted_lines = 0
+                    if pending_content is not None:
+                        deleted_lines = _text_line_count(pending_content)
+                    else:
+                        raw = source.read_bytes()
+                        try:
+                            deleted_lines = _text_line_count(raw.decode("utf-8"))
+                        except UnicodeDecodeError:
+                            deleted_lines = 0
+                    deletes.add(source)
+                    writes.pop(source, None)
+                    summaries.append(_PatchSummary(
+                        action="delete",
+                        path=op.path,
+                        deleted=deleted_lines,
+                    ))
+                    continue
+
+                pending_content = writes.get(source)
+                if pending_content is None and not source.exists():
+                    raise _PatchError(f"file to update does not exist: {op.path}")
+                if pending_content is None and not source.is_file():
+                    raise _PatchError(f"path to update is not a file: {op.path}")
+                if pending_content is not None:
+                    content = pending_content
+                else:
+                    raw = source.read_bytes()
+                    try:
+                        content = raw.decode("utf-8")
+                    except UnicodeDecodeError as exc:
+                        raise _PatchError(f"file to update is not UTF-8 text: {op.path}") from exc
+                uses_crlf = "\r\n" in content
+                content = content.replace("\r\n", "\n")
+                new_content = _apply_hunks(op.path, content, op.hunks or [])
+                added, deleted = _line_diff_stats(content, new_content)
+                if uses_crlf:
+                    new_content = new_content.replace("\n", "\r\n")
+
+                target = self._resolve(op.new_path) if op.new_path else source
+                if op.new_path and (target.exists() or target in writes) and target != source:
+                    raise _PatchError(f"move target already exists: {op.new_path}")
+                writes[target] = new_content
+                deletes.discard(target)
+                if target != source:
+                    deletes.add(source)
+                    writes.pop(source, None)
+                summaries.append(_PatchSummary(
+                    action="move" if op.new_path else "update",
+                    path=op.path,
+                    new_path=op.new_path,
+                    added=added,
+                    deleted=deleted,
+                ))
+
+            if dry_run:
+                return (
+                    "Patch dry-run succeeded:\n"
+                    + "\n".join(_format_summary(summary) for summary in summaries)
+                )
+
+            backups: dict[Path, bytes | None] = {}
+            for path in set(writes) | deletes:
+                backups[path] = path.read_bytes() if path.exists() else None
+
+            try:
+                for path in deletes:
+                    if path.exists():
+                        path.unlink()
+                for path, content in writes.items():
+                    path.parent.mkdir(parents=True, exist_ok=True)
+                    path.write_text(content, encoding="utf-8", newline="")
+            except Exception:
+                for path, data in backups.items():
+                    if data is None:
+                        if path.exists():
+                            path.unlink()
+                    else:
+                        path.parent.mkdir(parents=True, exist_ok=True)
+                        path.write_bytes(data)
+                raise
+
+            for path in set(writes) | deletes:
+                self._file_states.record_write(path)
+            return (
+                "Patch applied:\n"
+                + "\n".join(_format_summary(summary) for summary in summaries)
+            )
+        except PermissionError as exc:
+            return f"Error: {exc}"
+        except _PatchError as exc:
+            return f"Error applying patch: {exc}"
+        except Exception as exc:
+            return f"Error applying patch: {exc}"

nanobot/agent/tools/exec_session.py

@@ -0,0 +1,591 @@
+"""Session support for long-running exec workflows."""
+
+from __future__ import annotations
+
+import asyncio
+import shutil
+import time
+import uuid
+from contextlib import suppress
+from dataclasses import dataclass
+from typing import Any
+
+from nanobot.agent.tools.base import Tool, tool_parameters
+from nanobot.agent.tools.schema import BooleanSchema, IntegerSchema, StringSchema, tool_parameters_schema
+
+
+DEFAULT_YIELD_MS = 1000
+MAX_YIELD_MS = 30_000
+DEFAULT_WAIT_FOR_MS = 10_000
+MAX_WAIT_FOR_MS = 120_000
+DEFAULT_MAX_OUTPUT_CHARS = 10_000
+MAX_OUTPUT_CHARS = 50_000
+
+
+@dataclass(slots=True)
+class _SessionPoll:
+    output: str
+    done: bool
+    exit_code: int | None
+    elapsed_s: float = 0.0
+    timed_out: bool = False
+    terminated: bool = False
+    stdin_closed: bool = False
+    truncated_chars: int = 0
+
+
+@dataclass(slots=True)
+class ExecSessionInfo:
+    session_id: str
+    command: str
+    cwd: str
+    elapsed_s: float
+    idle_s: float
+    remaining_s: float
+    returncode: int | None
+
+
+class _ExecSession:
+    def __init__(
+        self,
+        *,
+        session_id: str,
+        process: asyncio.subprocess.Process,
+        command: str,
+        cwd: str,
+        timeout: int,
+    ) -> None:
+        self.session_id = session_id
+        self.process = process
+        self.command = command
+        self.cwd = cwd
+        self.started_at = time.monotonic()
+        self.deadline = time.monotonic() + timeout
+        self.last_access = time.monotonic()
+        self._chunks: list[str] = []
+        self._lock = asyncio.Lock()
+        self._timed_out = False
+        self._stdout_task = asyncio.create_task(self._read_stream(process.stdout, ""))
+        self._stderr_task = asyncio.create_task(self._read_stream(process.stderr, "STDERR:\n"))
+
+    async def _read_stream(
+        self,
+        stream: asyncio.StreamReader | None,
+        prefix: str,
+    ) -> None:
+        if stream is None:
+            return
+        first = True
+        while True:
+            chunk = await stream.read(4096)
+            if not chunk:
+                break
+            text = chunk.decode("utf-8", errors="replace")
+            if prefix and first:
+                text = prefix + text
+                first = False
+            async with self._lock:
+                self._chunks.append(text)
+
+    async def write(self, chars: str) -> str | None:
+        if self.process.returncode is not None:
+            return "session has already exited"
+        if self.process.stdin is None:
+            return "session stdin is not available"
+        try:
+            self.process.stdin.write(chars.encode("utf-8"))
+            await self.process.stdin.drain()
+        except (BrokenPipeError, ConnectionResetError):
+            return "session stdin is closed"
+        return None
+
+    async def close_stdin(self) -> str | None:
+        if self.process.returncode is not None:
+            return "session has already exited"
+        if self.process.stdin is None:
+            return "session stdin is not available"
+        self.process.stdin.close()
+        with suppress(BrokenPipeError, ConnectionResetError):
+            await self.process.stdin.wait_closed()
+        return None
+
+    async def poll(
+        self,
+        yield_time_ms: int,
+        max_output_chars: int,
+        *,
+        terminated: bool = False,
+        stdin_closed: bool = False,
+    ) -> _SessionPoll:
+        self.last_access = time.monotonic()
+        if yield_time_ms > 0 and self.process.returncode is None:
+            await asyncio.sleep(min(yield_time_ms, MAX_YIELD_MS) / 1000)
+
+        if self.process.returncode is None and time.monotonic() >= self.deadline:
+            self._timed_out = True
+            await self.kill()
+
+        if self.process.returncode is not None:
+            with suppress(asyncio.TimeoutError):
+                await asyncio.wait_for(
+                    asyncio.gather(self._stdout_task, self._stderr_task),
+                    timeout=2.0,
+                )
+
+        async with self._lock:
+            output = "".join(self._chunks)
+            self._chunks.clear()
+
+        output, truncated = _truncate_output(output, max_output_chars)
+        return _SessionPoll(
+            output=output,
+            done=self.process.returncode is not None,
+            exit_code=self.process.returncode,
+            elapsed_s=max(0.0, time.monotonic() - self.started_at),
+            timed_out=self._timed_out,
+            terminated=terminated,
+            stdin_closed=stdin_closed,
+            truncated_chars=truncated,
+        )
+
+    async def kill(self) -> None:
+        if self.process.returncode is not None:
+            return
+        self.process.kill()
+        with suppress(asyncio.TimeoutError):
+            await asyncio.wait_for(self.process.wait(), timeout=5.0)
+
+
+class ExecSessionManager:
+    def __init__(self, *, max_sessions: int = 8, idle_timeout: int = 1800) -> None:
+        self.max_sessions = max_sessions
+        self.idle_timeout = idle_timeout
+        self._sessions: dict[str, _ExecSession] = {}
+        self._lock = asyncio.Lock()
+
+    async def start(
+        self,
+        *,
+        command: str,
+        cwd: str,
+        env: dict[str, str],
+        timeout: int,
+        shell_program: str | None,
+        login: bool,
+        yield_time_ms: int,
+        max_output_chars: int,
+    ) -> tuple[str, _SessionPoll]:
+        async with self._lock:
+            await self._cleanup_locked()
+            if len(self._sessions) >= self.max_sessions:
+                raise RuntimeError(f"maximum exec sessions reached ({self.max_sessions})")
+            process = await self._spawn(command, cwd, env, shell_program, login)
+            session_id = uuid.uuid4().hex[:12]
+            session = _ExecSession(
+                session_id=session_id,
+                process=process,
+                command=command,
+                cwd=cwd,
+                timeout=timeout,
+            )
+            self._sessions[session_id] = session
+
+        poll = await session.poll(yield_time_ms, max_output_chars)
+        if poll.done:
+            async with self._lock:
+                self._sessions.pop(session_id, None)
+        return session_id, poll
+
+    async def write(
+        self,
+        *,
+        session_id: str,
+        chars: str | None,
+        close_stdin: bool,
+        terminate: bool,
+        yield_time_ms: int,
+        max_output_chars: int,
+    ) -> _SessionPoll:
+        async with self._lock:
+            await self._cleanup_locked()
+            session = self._sessions.get(session_id)
+        if session is None:
+            raise KeyError(session_id)
+
+        if chars:
+            error = await session.write(chars)
+            if error:
+                raise RuntimeError(error)
+        stdin_closed = False
+        if close_stdin:
+            error = await session.close_stdin()
+            if error:
+                raise RuntimeError(error)
+            stdin_closed = True
+        if terminate:
+            await session.kill()
+        poll = await session.poll(
+            yield_time_ms,
+            max_output_chars,
+            terminated=terminate,
+            stdin_closed=stdin_closed,
+        )
+        if poll.done:
+            async with self._lock:
+                self._sessions.pop(session_id, None)
+        return poll
+
+    async def list(self) -> list[ExecSessionInfo]:
+        async with self._lock:
+            await self._cleanup_locked()
+            now = time.monotonic()
+            return [
+                ExecSessionInfo(
+                    session_id=session_id,
+                    command=session.command,
+                    cwd=session.cwd,
+                    elapsed_s=max(0.0, now - session.started_at),
+                    idle_s=max(0.0, now - session.last_access),
+                    remaining_s=max(0.0, session.deadline - now),
+                    returncode=session.process.returncode,
+                )
+                for session_id, session in sorted(self._sessions.items())
+            ]
+
+    async def _cleanup_locked(self) -> None:
+        now = time.monotonic()
+        stale = [
+            session_id
+            for session_id, session in self._sessions.items()
+            if now - session.last_access > self.idle_timeout
+        ]
+        for session_id in stale:
+            session = self._sessions.pop(session_id)
+            await session.kill()
+
+    async def _spawn(
+        self,
+        command: str,
+        cwd: str,
+        env: dict[str, str],
+        shell_program: str | None,
+        login: bool,
+    ) -> asyncio.subprocess.Process:
+        from nanobot.agent.tools import shell
+
+        if shell._IS_WINDOWS:
+            return await asyncio.create_subprocess_shell(
+                command,
+                stdin=asyncio.subprocess.PIPE,
+                stdout=asyncio.subprocess.PIPE,
+                stderr=asyncio.subprocess.PIPE,
+                cwd=cwd,
+                env=env,
+            )
+        shell_program = shell_program or shutil.which("bash") or "/bin/bash"
+        args = [shell_program]
+        if login and shell_program.rsplit("/", 1)[-1] in {"bash", "zsh"}:
+            args.append("-l")
+        args.extend(["-c", command])
+        return await asyncio.create_subprocess_exec(
+            *args,
+            stdin=asyncio.subprocess.PIPE,
+            stdout=asyncio.subprocess.PIPE,
+            stderr=asyncio.subprocess.PIPE,
+            cwd=cwd,
+            env=env,
+        )
+
+
+DEFAULT_EXEC_SESSION_MANAGER = ExecSessionManager()
+
+
+def clamp_session_int(value: int | None, default: int, minimum: int, maximum: int) -> int:
+    if value is None:
+        return default
+    return min(max(value, minimum), maximum)
+
+
+def _truncate_output(output: str, max_output_chars: int) -> tuple[str, int]:
+    if len(output) <= max_output_chars:
+        return output, 0
+    half = max_output_chars // 2
+    omitted = len(output) - max_output_chars
+    return (
+        output[:half]
+        + f"\n\n... ({omitted:,} chars truncated) ...\n\n"
+        + output[-half:],
+        omitted,
+    )
+
+
+def format_session_poll(session_id: str, poll: _SessionPoll) -> str:
+    parts = [poll.output] if poll.output else []
+    if poll.truncated_chars:
+        parts.append(f"(output truncated by {poll.truncated_chars:,} chars)")
+    if poll.timed_out:
+        parts.append("Error: Command timed out; session was terminated.")
+    if poll.terminated and not poll.timed_out:
+        parts.append("Session terminated.")
+    if poll.stdin_closed:
+        parts.append("Stdin closed.")
+    if poll.done:
+        parts.append(f"Exit code: {poll.exit_code}")
+    else:
+        parts.append(f"Process running. session_id: {session_id}")
+    parts.append(f"Elapsed: {poll.elapsed_s:.1f}s")
+    return "\n".join(parts) if parts else "(no output yet)"
+
+
+@tool_parameters(
+    tool_parameters_schema(
+        session_id=StringSchema("Session id returned by exec when yield_time_ms is used."),
+        chars=StringSchema(
+            "Bytes/text to write to stdin. Omit or pass an empty string to only poll recent output.",
+            nullable=True,
+        ),
+        close_stdin=BooleanSchema(
+            description="Close stdin after writing chars. Useful for commands waiting for EOF.",
+            default=False,
+        ),
+        terminate=BooleanSchema(
+            description="Terminate the running exec session.",
+            default=False,
+        ),
+        yield_time_ms=IntegerSchema(
+            DEFAULT_YIELD_MS,
+            description="Milliseconds to wait before returning recent output (default 1000, max 30000).",
+            minimum=0,
+            maximum=MAX_YIELD_MS,
+        ),
+        wait_for=StringSchema(
+            "Optional text to wait for in output before returning. "
+            "Useful for interactive commands and dev servers.",
+            nullable=True,
+        ),
+        wait_timeout_ms=IntegerSchema(
+            DEFAULT_WAIT_FOR_MS,
+            description="Maximum milliseconds to wait for wait_for text (default 10000, max 120000).",
+            minimum=0,
+            maximum=MAX_WAIT_FOR_MS,
+            nullable=True,
+        ),
+        max_output_chars=IntegerSchema(
+            DEFAULT_MAX_OUTPUT_CHARS,
+            description="Maximum output characters to return from this poll (default 10000, max 50000).",
+            minimum=1000,
+            maximum=MAX_OUTPUT_CHARS,
+        ),
+        max_output_tokens=IntegerSchema(
+            DEFAULT_MAX_OUTPUT_CHARS,
+            description="Compatibility alias for max_output_chars. The current runtime uses a character budget.",
+            minimum=1000,
+            maximum=MAX_OUTPUT_CHARS,
+            nullable=True,
+        ),
+        required=["session_id"],
+    )
+)
+class WriteStdinTool(Tool):
+    """Write to or poll a running exec session."""
+
+    _scopes = {"core", "subagent"}
+    config_key = "exec"
+
+    @classmethod
+    def config_cls(cls):
+        from nanobot.agent.tools.shell import ExecToolConfig
+
+        return ExecToolConfig
+
+    @classmethod
+    def enabled(cls, ctx: Any) -> bool:
+        return ctx.config.exec.enable
+
+    def __init__(
+        self,
+        *,
+        manager: ExecSessionManager | None = None,
+    ) -> None:
+        self._manager = manager or DEFAULT_EXEC_SESSION_MANAGER
+
+    @classmethod
+    def create(cls, ctx: Any) -> Tool:
+        return cls()
+
+    @property
+    def exclusive(self) -> bool:
+        return True
+
+    @property
+    def name(self) -> str:
+        return "write_stdin"
+
+    @property
+    def description(self) -> str:
+        return (
+            "Interact with a running exec session created by exec with "
+            "yield_time_ms. Use chars='' to poll without writing, chars to send "
+            "stdin, close_stdin=true to send EOF, or terminate=true to stop the "
+            "process. Use wait_for with wait_timeout_ms for dev servers, test "
+            "watchers, and prompts where you need to wait for expected output. "
+            "Do not use this to start new commands; start them with exec."
+        )
+
+    async def execute(
+        self,
+        session_id: str,
+        chars: str | None = None,
+        close_stdin: bool = False,
+        terminate: bool = False,
+        yield_time_ms: int | None = None,
+        wait_for: str | None = None,
+        wait_timeout_ms: int | None = None,
+        max_output_chars: int | None = None,
+        max_output_tokens: int | None = None,
+        **kwargs: Any,
+    ) -> str:
+        try:
+            if max_output_chars is None:
+                max_output_chars = max_output_tokens
+            output_limit = clamp_session_int(
+                max_output_chars,
+                DEFAULT_MAX_OUTPUT_CHARS,
+                1000,
+                MAX_OUTPUT_CHARS,
+            )
+            if wait_for:
+                return await self._wait_for_output(
+                    session_id=session_id,
+                    chars=chars,
+                    close_stdin=close_stdin,
+                    terminate=terminate,
+                    wait_for=wait_for,
+                    wait_timeout_ms=clamp_session_int(
+                        wait_timeout_ms,
+                        DEFAULT_WAIT_FOR_MS,
+                        0,
+                        MAX_WAIT_FOR_MS,
+                    ),
+                    max_output_chars=output_limit,
+                )
+            poll = await self._manager.write(
+                session_id=session_id,
+                chars=chars,
+                close_stdin=close_stdin,
+                terminate=terminate,
+                yield_time_ms=clamp_session_int(yield_time_ms, DEFAULT_YIELD_MS, 0, MAX_YIELD_MS),
+                max_output_chars=output_limit,
+            )
+            return format_session_poll(session_id, poll)
+        except KeyError:
+            return f"Error: exec session not found: {session_id}"
+        except Exception as exc:
+            return f"Error writing to exec session: {exc}"
+
+    async def _wait_for_output(
+        self,
+        *,
+        session_id: str,
+        chars: str | None,
+        close_stdin: bool,
+        terminate: bool,
+        wait_for: str,
+        wait_timeout_ms: int,
+        max_output_chars: int,
+    ) -> str:
+        deadline = time.monotonic() + (wait_timeout_ms / 1000)
+        aggregate: list[str] = []
+        first = True
+        poll: _SessionPoll | None = None
+
+        while True:
+            remaining_ms = max(0, int((deadline - time.monotonic()) * 1000))
+            step_ms = min(500, remaining_ms)
+            poll = await self._manager.write(
+                session_id=session_id,
+                chars=chars if first else None,
+                close_stdin=close_stdin if first else False,
+                terminate=terminate if first else False,
+                yield_time_ms=step_ms,
+                max_output_chars=max_output_chars,
+            )
+            first = False
+            if poll.output:
+                aggregate.append(poll.output)
+                joined = "".join(aggregate)
+                if wait_for in joined:
+                    poll.output = joined
+                    return format_session_poll(session_id, poll)
+            if poll.done or remaining_ms <= 0:
+                poll.output = "".join(aggregate)
+                result = format_session_poll(session_id, poll)
+                if wait_for not in poll.output:
+                    result += f"\nWait target not observed: {wait_for!r}"
+                return result
+
+
+@tool_parameters(tool_parameters_schema())
+class ListExecSessionsTool(Tool):
+    """List active exec sessions."""
+
+    _scopes = {"core", "subagent"}
+    config_key = "exec"
+
+    @classmethod
+    def config_cls(cls):
+        from nanobot.agent.tools.shell import ExecToolConfig
+
+        return ExecToolConfig
+
+    @classmethod
+    def enabled(cls, ctx: Any) -> bool:
+        return ctx.config.exec.enable
+
+    def __init__(
+        self,
+        *,
+        manager: ExecSessionManager | None = None,
+    ) -> None:
+        self._manager = manager or DEFAULT_EXEC_SESSION_MANAGER
+
+    @classmethod
+    def create(cls, ctx: Any) -> Tool:
+        return cls()
+
+    @property
+    def name(self) -> str:
+        return "list_exec_sessions"
+
+    @property
+    def description(self) -> str:
+        return (
+            "List active long-running exec sessions, including session_id, cwd, "
+            "elapsed time, idle time, remaining timeout, and command preview. "
+            "Use this to recover a session_id after context shifts before "
+            "polling, writing stdin, or terminating with write_stdin."
+        )
+
+    @property
+    def read_only(self) -> bool:
+        return True
+
+    async def execute(self, **kwargs: Any) -> str:
+        try:
+            sessions = await self._manager.list()
+            if not sessions:
+                return "No active exec sessions."
+            lines = []
+            for info in sessions:
+                command = " ".join(info.command.split())
+                if len(command) > 120:
+                    command = command[:119] + "..."
+                status = "exited" if info.returncode is not None else "running"
+                lines.append(
+                    f"{info.session_id} | {status} | elapsed={info.elapsed_s:.1f}s "
+                    f"| idle={info.idle_s:.1f}s | remaining={info.remaining_s:.1f}s "
+                    f"| cwd={info.cwd} | {command}"
+                )
+            return "\n".join(lines)
+        except Exception as exc:
+            return f"Error listing exec sessions: {exc}"

nanobot/agent/tools/filesystem.py

@@ -132,6 +132,10 @@ def _parse_page_range(pages: str, total: int) -> tuple[int, int]:
             minimum=1,
         ),
         pages=StringSchema("Page range for PDF files, e.g. '1-5' (default: all, max 20 pages)"),
+        force=BooleanSchema(
+            description="Bypass same-file read deduplication and return content again.",
+            default=False,
+        ),
         required=["path"],
     )
 )
@@ -154,7 +158,11 @@ class ReadFileTool(_FsTool):
             "Text output format: LINE_NUM|CONTENT. "
             "Images return visual content for analysis. "
             "Supports PDF, DOCX, XLSX, PPTX documents. "
+            "Use find_files/list_dir first when the path is uncertain. "
+            "Read the relevant range before editing so replacements or patches "
+            "are based on current content. "
             "Use offset and limit for large text files. "
+            "Use force=true to re-read content even if unchanged. "
             "Reads exceeding ~128K chars are truncated."
         )
 
@@ -162,7 +170,15 @@ class ReadFileTool(_FsTool):
     def read_only(self) -> bool:
         return True
 
-    async def execute(self, path: str | None = None, offset: int = 1, limit: int | None = None, pages: str | None = None, **kwargs: Any) -> Any:
+    async def execute(
+        self,
+        path: str | None = None,
+        offset: int = 1,
+        limit: int | None = None,
+        pages: str | None = None,
+        force: bool = False,
+        **kwargs: Any,
+    ) -> Any:
         try:
             if not path:
                 return "Error reading file: Unknown path"
@@ -202,7 +218,13 @@ class ReadFileTool(_FsTool):
                 current_mtime = os.path.getmtime(fp)
             except OSError:
                 current_mtime = 0.0
-            if entry and entry.can_dedup and entry.offset == offset and entry.limit == limit:
+            if (
+                not force
+                and entry
+                and entry.can_dedup
+                and entry.offset == offset
+                and entry.limit == limit
+            ):
                 if current_mtime != entry.mtime:
                     # File was modified externally - force full read and mark as not dedupable
                     entry.can_dedup = False
@@ -365,9 +387,10 @@ class WriteFileTool(_FsTool):
     @property
     def description(self) -> str:
         return (
-            "Write content to a file. Overwrites if the file already exists; "
+            "Create a new file or intentionally replace an entire file with "
-            "creates parent directories as needed. "
+            "the provided content. Overwrites existing files and creates parent "
-            "For partial edits, prefer edit_file instead."
+            "directories as needed. For code changes or partial edits, prefer "
+            "apply_patch; use edit_file only for small exact replacements."
         )
 
     async def execute(self, path: str | None = None, content: str | None = None, **kwargs: Any) -> str:
@@ -657,6 +680,24 @@ def _find_match(content: str, old_text: str) -> tuple[str | None, int]:
         old_text=StringSchema("The text to find and replace"),
         new_text=StringSchema("The text to replace with"),
         replace_all=BooleanSchema(description="Replace all occurrences (default false)"),
+        occurrence=IntegerSchema(
+            1,
+            description="Optional 1-based occurrence to replace when old_text appears multiple times.",
+            minimum=1,
+            nullable=True,
+        ),
+        line_hint=IntegerSchema(
+            1,
+            description="Optional 1-based line hint used to choose the nearest match.",
+            minimum=1,
+            nullable=True,
+        ),
+        expected_replacements=IntegerSchema(
+            1,
+            description="Optional guard for the number of replacements that must be made.",
+            minimum=1,
+            nullable=True,
+        ),
         required=["path", "old_text", "new_text"],
     )
 )
@@ -674,10 +715,13 @@ class EditFileTool(_FsTool):
     @property
     def description(self) -> str:
         return (
-            "Edit a file by replacing old_text with new_text. "
+            "Perform a small, exact replacement in one file by replacing "
-            "Tolerates minor whitespace/indentation differences and curly/straight quote mismatches. "
+            "old_text with new_text. Use this for narrow text substitutions "
-            "If old_text matches multiple times, you must provide more context "
+            "with old_text copied from read_file. For multi-file, structural, "
-            "or set replace_all=true. Shows a diff of the closest match on failure."
+            "or generated code edits, prefer apply_patch. If old_text matches "
+            "multiple times, provide more context or set occurrence, line_hint, "
+            "replace_all, and expected_replacements. Shows closest-match "
+            "diagnostics on failure."
         )
 
     @staticmethod
@@ -688,7 +732,8 @@ class EditFileTool(_FsTool):
     async def execute(
         self, path: str | None = None, old_text: str | None = None,
         new_text: str | None = None,
-        replace_all: bool = False, **kwargs: Any,
+        replace_all: bool = False, occurrence: int | None = None,
+        line_hint: int | None = None, expected_replacements: int | None = None, **kwargs: Any,
     ) -> str:
         try:
             if not path:
@@ -697,10 +742,12 @@ class EditFileTool(_FsTool):
                 raise ValueError("Unknown old_text")
             if new_text is None:
                 raise ValueError("Unknown new_text")
-
+            if occurrence is not None and occurrence < 1:
-            # .ipynb detection
+                return "Error: occurrence must be >= 1."
-            if path.endswith(".ipynb"):
+            if line_hint is not None and line_hint < 1:
-                return "Error: This is a Jupyter notebook. Use the notebook_edit tool instead of edit_file."
+                return "Error: line_hint must be >= 1."
+            if expected_replacements is not None and expected_replacements < 1:
+                return "Error: expected_replacements must be >= 1."
 
             fp = self._resolve(path)
 
@@ -743,7 +790,28 @@ class EditFileTool(_FsTool):
             if not matches:
                 return self._not_found_msg(old_text, content, path)
             count = len(matches)
+            if replace_all and occurrence is not None:
+                return "Error: occurrence cannot be used with replace_all=true."
+            if replace_all and line_hint is not None:
+                return "Error: line_hint cannot be used with replace_all=true."
+            if occurrence is not None and line_hint is not None:
+                return "Error: line_hint cannot be used with occurrence."
             if count > 1 and not replace_all:
+                if occurrence is not None:
+                    if occurrence > count:
+                        return (
+                            f"Error: occurrence {occurrence} is out of range; "
+                            f"old_text appears {count} times."
+                        )
+                elif line_hint is not None:
+                    nearest = min(matches, key=lambda match: abs(match.line - line_hint))
+                    distance = abs(nearest.line - line_hint)
+                    if sum(1 for match in matches if abs(match.line - line_hint) == distance) > 1:
+                        return (
+                            f"Error: line_hint {line_hint} is ambiguous; "
+                            f"old_text appears {count} times."
+                        )
+                else:
                     line_numbers = [match.line for match in matches]
                     preview = ", ".join(f"line {n}" for n in line_numbers[:3])
                     if len(line_numbers) > 3:
@@ -751,7 +819,13 @@ class EditFileTool(_FsTool):
                     location_hint = f" at {preview}" if preview else ""
                     return (
                         f"Warning: old_text appears {count} times{location_hint}. "
-                    "Provide more context to make it unique, or set replace_all=true."
+                        "Provide more context, set occurrence to choose one match, "
+                        "or set replace_all=true."
+                    )
+            elif occurrence is not None and occurrence > count:
+                return (
+                    f"Error: occurrence {occurrence} is out of range; "
+                    f"old_text appears {count} time."
                 )
 
             norm_new = new_text.replace("\r\n", "\n")
@@ -760,7 +834,17 @@ class EditFileTool(_FsTool):
             if fp.suffix.lower() not in self._MARKDOWN_EXTS:
                 norm_new = self._strip_trailing_ws(norm_new)
 
-            selected = matches if replace_all else matches[:1]
+            if replace_all:
+                selected = matches
+            elif line_hint is not None:
+                selected = [min(matches, key=lambda match: abs(match.line - line_hint))]
+            else:
+                selected = [matches[occurrence - 1 if occurrence else 0]]
+            if expected_replacements is not None and len(selected) != expected_replacements:
+                return (
+                    f"Error: expected {expected_replacements} replacements but "
+                    f"would make {len(selected)}."
+                )
             new_content = content
             for match in reversed(selected):
                 replacement = _preserve_quote_style(norm_old, match.text, norm_new)

nanobot/agent/tools/notebook.py

@@ -1,162 +0,0 @@
-"""NotebookEditTool — edit Jupyter .ipynb notebooks."""
-
-from __future__ import annotations
-
-import json
-import uuid
-from typing import Any
-
-from nanobot.agent.tools.base import tool_parameters
-from nanobot.agent.tools.schema import IntegerSchema, StringSchema, tool_parameters_schema
-from nanobot.agent.tools.filesystem import _FsTool
-
-
-def _new_cell(source: str, cell_type: str = "code", generate_id: bool = False) -> dict:
-    cell: dict[str, Any] = {
-        "cell_type": cell_type,
-        "source": source,
-        "metadata": {},
-    }
-    if cell_type == "code":
-        cell["outputs"] = []
-        cell["execution_count"] = None
-    if generate_id:
-        cell["id"] = uuid.uuid4().hex[:8]
-    return cell
-
-
-def _make_empty_notebook() -> dict:
-    return {
-        "nbformat": 4,
-        "nbformat_minor": 5,
-        "metadata": {
-            "kernelspec": {"display_name": "Python 3", "language": "python", "name": "python3"},
-            "language_info": {"name": "python"},
-        },
-        "cells": [],
-    }
-
-
-@tool_parameters(
-    tool_parameters_schema(
-        path=StringSchema("Path to the .ipynb notebook file"),
-        cell_index=IntegerSchema(0, description="0-based index of the cell to edit", minimum=0),
-        new_source=StringSchema("New source content for the cell"),
-        cell_type=StringSchema(
-            "Cell type: 'code' or 'markdown' (default: code)",
-            enum=["code", "markdown"],
-        ),
-        edit_mode=StringSchema(
-            "Mode: 'replace' (default), 'insert' (after target), or 'delete'",
-            enum=["replace", "insert", "delete"],
-        ),
-        required=["path", "cell_index"],
-    )
-)
-class NotebookEditTool(_FsTool):
-    """Edit Jupyter notebook cells: replace, insert, or delete."""
-    _scopes = {"core"}
-
-    _VALID_CELL_TYPES = frozenset({"code", "markdown"})
-    _VALID_EDIT_MODES = frozenset({"replace", "insert", "delete"})
-
-    @property
-    def name(self) -> str:
-        return "notebook_edit"
-
-    @property
-    def description(self) -> str:
-        return (
-            "Edit a Jupyter notebook (.ipynb) cell. "
-            "Modes: replace (default) replaces cell content, "
-            "insert adds a new cell after the target index, "
-            "delete removes the cell at the index. "
-            "cell_index is 0-based."
-        )
-
-    async def execute(
-        self,
-        path: str | None = None,
-        cell_index: int = 0,
-        new_source: str = "",
-        cell_type: str = "code",
-        edit_mode: str = "replace",
-        **kwargs: Any,
-    ) -> str:
-        try:
-            if not path:
-                return "Error: path is required"
-
-            if not path.endswith(".ipynb"):
-                return "Error: notebook_edit only works on .ipynb files. Use edit_file for other files."
-
-            if edit_mode not in self._VALID_EDIT_MODES:
-                return (
-                    f"Error: Invalid edit_mode '{edit_mode}'. "
-                    "Use one of: replace, insert, delete."
-                )
-
-            if cell_type not in self._VALID_CELL_TYPES:
-                return (
-                    f"Error: Invalid cell_type '{cell_type}'. "
-                    "Use one of: code, markdown."
-                )
-
-            fp = self._resolve(path)
-
-            # Create new notebook if file doesn't exist and mode is insert
-            if not fp.exists():
-                if edit_mode != "insert":
-                    return f"Error: File not found: {path}"
-                nb = _make_empty_notebook()
-                cell = _new_cell(new_source, cell_type, generate_id=True)
-                nb["cells"].append(cell)
-                fp.parent.mkdir(parents=True, exist_ok=True)
-                fp.write_text(json.dumps(nb, indent=1, ensure_ascii=False), encoding="utf-8")
-                return f"Successfully created {fp} with 1 cell"
-
-            try:
-                nb = json.loads(fp.read_text(encoding="utf-8"))
-            except (json.JSONDecodeError, UnicodeDecodeError) as e:
-                return f"Error: Failed to parse notebook: {e}"
-
-            cells = nb.get("cells", [])
-            nbformat_minor = nb.get("nbformat_minor", 0)
-            generate_id = nb.get("nbformat", 0) >= 4 and nbformat_minor >= 5
-
-            if edit_mode == "delete":
-                if cell_index < 0 or cell_index >= len(cells):
-                    return f"Error: cell_index {cell_index} out of range (notebook has {len(cells)} cells)"
-                cells.pop(cell_index)
-                nb["cells"] = cells
-                fp.write_text(json.dumps(nb, indent=1, ensure_ascii=False), encoding="utf-8")
-                return f"Successfully deleted cell {cell_index} from {fp}"
-
-            if edit_mode == "insert":
-                insert_at = min(cell_index + 1, len(cells))
-                cell = _new_cell(new_source, cell_type, generate_id=generate_id)
-                cells.insert(insert_at, cell)
-                nb["cells"] = cells
-                fp.write_text(json.dumps(nb, indent=1, ensure_ascii=False), encoding="utf-8")
-                return f"Successfully inserted cell at index {insert_at} in {fp}"
-
-            # Default: replace
-            if cell_index < 0 or cell_index >= len(cells):
-                return f"Error: cell_index {cell_index} out of range (notebook has {len(cells)} cells)"
-            cells[cell_index]["source"] = new_source
-            if cell_type and cells[cell_index].get("cell_type") != cell_type:
-                cells[cell_index]["cell_type"] = cell_type
-                if cell_type == "code":
-                    cells[cell_index].setdefault("outputs", [])
-                    cells[cell_index].setdefault("execution_count", None)
-                elif "outputs" in cells[cell_index]:
-                    del cells[cell_index]["outputs"]
-                    cells[cell_index].pop("execution_count", None)
-            nb["cells"] = cells
-            fp.write_text(json.dumps(nb, indent=1, ensure_ascii=False), encoding="utf-8")
-            return f"Successfully edited cell {cell_index} in {fp}"
-
-        except PermissionError as e:
-            return f"Error: {e}"
-        except Exception as e:
-            return f"Error editing notebook: {e}"

nanobot/agent/tools/search.py

@@ -1,4 +1,4 @@
-"""Search tools: grep."""
+"""Search tools: file discovery and grep."""
 
 from __future__ import annotations
 
@@ -12,6 +12,7 @@ from typing import Any, Iterable, TypeVar
 from nanobot.agent.tools.filesystem import ListDirTool, _FsTool
 
 _DEFAULT_HEAD_LIMIT = 250
+_DEFAULT_FILE_HEAD_LIMIT = 200
 T = TypeVar("T")
 _TYPE_GLOB_MAP = {
     "py": ("*.py", "*.pyi"),
@@ -88,6 +89,14 @@ def _matches_type(name: str, file_type: str | None) -> bool:
     return any(fnmatch.fnmatch(name.lower(), pattern.lower()) for pattern in patterns)
 
 
+def _matches_query(rel_path: str, query: str | None) -> bool:
+    if not query:
+        return True
+    haystack = rel_path.lower()
+    terms = [part for part in query.lower().split() if part]
+    return all(term in haystack for term in terms)
+
+
 class _SearchTool(_FsTool):
     _IGNORE_DIRS = set(ListDirTool._IGNORE_DIRS)
 
@@ -109,6 +118,163 @@ class _SearchTool(_FsTool):
                 yield current / filename
 
 
+class FindFilesTool(_SearchTool):
+    """Find files by path fragment, glob, or type."""
+    _scopes = {"core", "subagent"}
+
+    @property
+    def name(self) -> str:
+        return "find_files"
+
+    @property
+    def description(self) -> str:
+        return (
+            "Find files by path fragment, glob, or file type. "
+            "Use this before read_file when you need to locate files, and "
+            "prefer it over shell find/ls for ordinary workspace discovery. "
+            "Returns workspace-relative paths and skips common dependency/build "
+            "directories."
+        )
+
+    @property
+    def read_only(self) -> bool:
+        return True
+
+    @property
+    def parameters(self) -> dict[str, Any]:
+        return {
+            "type": "object",
+            "properties": {
+                "path": {
+                    "type": "string",
+                    "description": "Directory or file to search in (default '.')",
+                },
+                "query": {
+                    "type": "string",
+                    "description": (
+                        "Optional case-insensitive path fragment search. "
+                        "Whitespace-separated terms must all be present."
+                    ),
+                },
+                "glob": {
+                    "type": "string",
+                    "description": "Optional file filter, e.g. '*.py' or 'tests/**/test_*.py'",
+                },
+                "type": {
+                    "type": "string",
+                    "description": "Optional file type shorthand, e.g. 'py', 'ts', 'md', 'json'",
+                },
+                "include_dirs": {
+                    "type": "boolean",
+                    "description": "Include matching directories as well as files (default false)",
+                },
+                "sort": {
+                    "type": "string",
+                    "enum": ["path", "modified"],
+                    "description": "Sort by path or most recently modified first (default path)",
+                },
+                "head_limit": {
+                    "type": "integer",
+                    "description": "Maximum number of paths to return (default 200, 0 for all, max 1000)",
+                    "minimum": 0,
+                    "maximum": 1000,
+                },
+                "offset": {
+                    "type": "integer",
+                    "description": "Skip the first N results before applying head_limit",
+                    "minimum": 0,
+                    "maximum": 100000,
+                },
+            },
+        }
+
+    def _iter_paths(self, root: Path, *, include_dirs: bool) -> Iterable[Path]:
+        if root.is_file():
+            yield root
+            return
+        if include_dirs:
+            yield root
+        for dirpath, dirnames, filenames in os.walk(root):
+            dirnames[:] = sorted(d for d in dirnames if d not in self._IGNORE_DIRS)
+            current = Path(dirpath)
+            if include_dirs and current != root:
+                yield current
+            for filename in sorted(filenames):
+                yield current / filename
+
+    async def execute(
+        self,
+        path: str = ".",
+        query: str | None = None,
+        glob: str | None = None,
+        type: str | None = None,
+        include_dirs: bool = False,
+        sort: str = "path",
+        head_limit: int | None = None,
+        offset: int = 0,
+        **kwargs: Any,
+    ) -> str:
+        try:
+            target = self._resolve(path or ".")
+            if not target.exists():
+                return f"Error: Path not found: {path}"
+            if not (target.is_dir() or target.is_file()):
+                return f"Error: Unsupported path: {path}"
+
+            if sort not in {"path", "modified"}:
+                return "Error: sort must be 'path' or 'modified'"
+
+            limit = (
+                _DEFAULT_FILE_HEAD_LIMIT
+                if head_limit is None
+                else None if head_limit == 0 else head_limit
+            )
+            root = target if target.is_dir() else target.parent
+            matches: list[tuple[str, float]] = []
+
+            for candidate in self._iter_paths(target, include_dirs=include_dirs):
+                if candidate.is_dir() and not include_dirs:
+                    continue
+                rel_path = candidate.relative_to(root).as_posix()
+                display_path = self._display_path(candidate, root)
+                name = candidate.name
+
+                if glob and not _match_glob(rel_path, name, glob):
+                    continue
+                if candidate.is_file() and not _matches_type(name, type):
+                    continue
+                if candidate.is_dir() and type:
+                    continue
+                if not _matches_query(display_path, query):
+                    continue
+                try:
+                    mtime = candidate.stat().st_mtime
+                except OSError:
+                    mtime = 0.0
+                suffix = "/" if candidate.is_dir() else ""
+                matches.append((display_path + suffix, mtime))
+
+            if sort == "modified":
+                matches.sort(key=lambda item: (-item[1], item[0]))
+            else:
+                matches.sort(key=lambda item: item[0])
+
+            paths = [item[0] for item in matches]
+            paged, truncated = _paginate(paths, limit, offset)
+            if not paged:
+                return "No files found"
+
+            result = "\n".join(paged)
+            note = _pagination_note(limit, offset, truncated)
+            if note:
+                result += "\n\n" + note
+            return result
+        except PermissionError as e:
+            return f"Error: {e}"
+        except Exception as e:
+            return f"Error finding files: {e}"
+
+
 class GrepTool(_SearchTool):
     """Search file contents using a regex-like pattern."""
     _scopes = {"core", "subagent"}
@@ -125,7 +291,8 @@ class GrepTool(_SearchTool):
         return (
             "Search file contents with a regex pattern. "
             "Default output_mode is files_with_matches (file paths only); "
-            "use content mode for matching lines with context. "
+            "use content mode for matching lines with context. Prefer this "
+            "over shell grep for ordinary workspace searches. "
             "Skips binary and files >2 MB. Supports glob/type filtering."
         )
 

nanobot/agent/tools/shell.py

@@ -8,6 +8,7 @@ import re
 import shutil
 import sys
 from contextlib import suppress
+from dataclasses import dataclass
 from pathlib import Path
 from typing import Any
 
@@ -15,8 +16,17 @@ from loguru import logger
 from pydantic import Field
 
 from nanobot.agent.tools.base import Tool, tool_parameters
+from nanobot.agent.tools.exec_session import (
+    DEFAULT_MAX_OUTPUT_CHARS,
+    DEFAULT_YIELD_MS,
+    DEFAULT_EXEC_SESSION_MANAGER,
+    MAX_OUTPUT_CHARS,
+    MAX_YIELD_MS,
+    clamp_session_int,
+    format_session_poll,
+)
 from nanobot.agent.tools.sandbox import wrap_command
-from nanobot.agent.tools.schema import IntegerSchema, StringSchema, tool_parameters_schema
+from nanobot.agent.tools.schema import BooleanSchema, IntegerSchema, StringSchema, tool_parameters_schema
 from nanobot.config.paths import get_media_dir
 from nanobot.config.schema import Base
 
@@ -44,10 +54,22 @@ class ExecToolConfig(Base):
     deny_patterns: list[str] = Field(default_factory=list)
 
 
+@dataclass(slots=True)
+class _PreparedCommand:
+    command: str
+    cwd: str
+    env: dict[str, str]
+    timeout: int
+    shell_program: str | None
+    login: bool
+
+
 @tool_parameters(
     tool_parameters_schema(
         command=StringSchema("The shell command to execute"),
+        cmd=StringSchema("Compatibility alias for command"),
         working_dir=StringSchema("Optional working directory for the command"),
+        workdir=StringSchema("Compatibility alias for working_dir"),
         timeout=IntegerSchema(
             60,
             description=(
@@ -57,7 +79,44 @@ class ExecToolConfig(Base):
             minimum=1,
             maximum=600,
         ),
-        required=["command"],
+        shell=StringSchema(
+            "Optional shell binary to launch. On Unix, supports sh, bash, or zsh.",
+            nullable=True,
+        ),
+        login=BooleanSchema(
+            description="Whether to run bash/zsh with login shell semantics (default true).",
+            default=True,
+            nullable=True,
+        ),
+        yield_time_ms=IntegerSchema(
+            description=(
+                "Optional milliseconds to wait before returning output. "
+                "When set, a still-running command returns a session_id that "
+                "can be polled or written to with write_stdin. Omit this field "
+                "to keep one-shot exec behavior."
+            ),
+            minimum=0,
+            maximum=MAX_YIELD_MS,
+            nullable=True,
+        ),
+        max_output_chars=IntegerSchema(
+            description=(
+                "Maximum output characters to return when yield_time_ms is used "
+                "(default 10000, max 50000)."
+            ),
+            minimum=1000,
+            maximum=MAX_OUTPUT_CHARS,
+            nullable=True,
+        ),
+        max_output_tokens=IntegerSchema(
+            description=(
+                "Compatibility alias for max_output_chars. The current runtime "
+                "uses a character budget."
+            ),
+            minimum=1000,
+            maximum=MAX_OUTPUT_CHARS,
+            nullable=True,
+        ),
     )
 )
 class ExecTool(Tool):
@@ -98,6 +157,7 @@ class ExecTool(Tool):
         sandbox: str = "",
         path_append: str = "",
         allowed_env_keys: list[str] | None = None,
+        session_manager: Any | None = None,
     ):
         self.timeout = timeout
         self.working_dir = working_dir
@@ -125,6 +185,7 @@ class ExecTool(Tool):
         self.restrict_to_workspace = restrict_to_workspace
         self.path_append = path_append
         self.allowed_env_keys = allowed_env_keys or []
+        self._session_manager = session_manager or DEFAULT_EXEC_SESSION_MANAGER
 
     @property
     def name(self) -> str:
@@ -150,10 +211,15 @@ class ExecTool(Tool):
     def description(self) -> str:
         return (
             "Execute a shell command and return its output. "
-            "Prefer read_file/write_file/edit_file over cat/echo/sed, "
+            "Use this for tests, builds, package commands, git commands, and "
-            "and grep/glob over shell find/grep. "
+            "other process execution. Prefer read_file/find_files/grep for "
+            "inspection and apply_patch/write_file/edit_file for file changes "
+            "instead of cat, shell find/grep, echo, or sed. "
             "Use -y or --yes flags to avoid interactive prompts. "
-            "Output is truncated at 10 000 chars; timeout defaults to 60s."
+            "For long-running or interactive commands, pass yield_time_ms; "
+            "if the command keeps running, exec returns a session_id that can "
+            "be polled or written to with write_stdin. Output is truncated at "
+            "10 000 chars; timeout defaults to 60s."
         )
 
     @property
@@ -161,9 +227,111 @@ class ExecTool(Tool):
         return True
 
     async def execute(
-        self, command: str, working_dir: str | None = None,
+        self, command: str | None = None, cmd: str | None = None,
-        timeout: int | None = None, **kwargs: Any,
+        working_dir: str | None = None, workdir: str | None = None,
+        timeout: int | None = None, shell: str | None = None,
+        login: bool | None = None, yield_time_ms: int | None = None,
+        max_output_chars: int | None = None,
+        max_output_tokens: int | None = None,
+        **kwargs: Any,
     ) -> str:
+        command = command or cmd
+        working_dir = working_dir or workdir
+        if not command:
+            return "Error: Missing command. Provide command or cmd."
+        if max_output_chars is None:
+            max_output_chars = max_output_tokens
+
+        prepared = self._prepare_command(command, working_dir, timeout, shell, login)
+        if isinstance(prepared, str):
+            return prepared
+
+        if yield_time_ms is not None:
+            return await self._execute_session(prepared, yield_time_ms, max_output_chars)
+
+        try:
+            process = await self._spawn(
+                prepared.command,
+                prepared.cwd,
+                prepared.env,
+                prepared.shell_program,
+                prepared.login,
+            )
+
+            try:
+                stdout, stderr = await asyncio.wait_for(
+                    process.communicate(),
+                    timeout=prepared.timeout,
+                )
+            except asyncio.TimeoutError:
+                await self._kill_process(process)
+                return f"Error: Command timed out after {prepared.timeout} seconds"
+            except asyncio.CancelledError:
+                await self._kill_process(process)
+                raise
+
+            output_parts = []
+
+            if stdout:
+                output_parts.append(stdout.decode("utf-8", errors="replace"))
+
+            if stderr:
+                stderr_text = stderr.decode("utf-8", errors="replace")
+                if stderr_text.strip():
+                    output_parts.append(f"STDERR:\n{stderr_text}")
+
+            output_parts.append(f"\nExit code: {process.returncode}")
+
+            result = "\n".join(output_parts) if output_parts else "(no output)"
+
+            max_len = clamp_session_int(max_output_chars, self._MAX_OUTPUT, 1000, MAX_OUTPUT_CHARS)
+            if len(result) > max_len:
+                half = max_len // 2
+                result = (
+                    result[:half]
+                    + f"\n\n... ({len(result) - max_len:,} chars truncated) ...\n\n"
+                    + result[-half:]
+                )
+
+            return result
+
+        except Exception as e:
+            return f"Error executing command: {str(e)}"
+
+    async def _execute_session(
+        self,
+        prepared: _PreparedCommand,
+        yield_time_ms: int | None,
+        max_output_chars: int | None,
+    ) -> str:
+        try:
+            session_id, poll = await self._session_manager.start(
+                command=prepared.command,
+                cwd=prepared.cwd,
+                env=prepared.env,
+                timeout=prepared.timeout,
+                shell_program=prepared.shell_program,
+                login=prepared.login,
+                yield_time_ms=clamp_session_int(yield_time_ms, DEFAULT_YIELD_MS, 0, MAX_YIELD_MS),
+                max_output_chars=clamp_session_int(
+                    max_output_chars,
+                    DEFAULT_MAX_OUTPUT_CHARS,
+                    1000,
+                    MAX_OUTPUT_CHARS,
+                ),
+            )
+            return format_session_poll(session_id, poll)
+        except Exception as exc:
+            return f"Error executing command: {exc}"
+
+    def _prepare_command(
+        self,
+        command: str,
+        working_dir: str | None = None,
+        timeout: int | None = None,
+        shell: str | None = None,
+        login: bool | None = None,
+    ) -> _PreparedCommand | str:
         cwd = working_dir or self.working_dir or os.getcwd()
 
         # Prevent an LLM-supplied working_dir from escaping the configured
@@ -211,52 +379,24 @@ class ExecTool(Tool):
                 env["NANOBOT_PATH_APPEND"] = self.path_append
                 command = f'export PATH="$PATH{os.pathsep}$NANOBOT_PATH_APPEND"; {command}'
 
-        try:
+        shell_program, shell_error = self._resolve_shell(shell)
-            process = await self._spawn(command, cwd, env)
+        if shell_error:
+            return shell_error
 
-            try:
+        return _PreparedCommand(
-                stdout, stderr = await asyncio.wait_for(
+            command=command,
-                    process.communicate(),
+            cwd=cwd,
+            env=env,
             timeout=effective_timeout,
+            shell_program=shell_program,
+            login=True if login is None else login,
         )
-            except asyncio.TimeoutError:
-                await self._kill_process(process)
-                return f"Error: Command timed out after {effective_timeout} seconds"
-            except asyncio.CancelledError:
-                await self._kill_process(process)
-                raise
-
-            output_parts = []
-
-            if stdout:
-                output_parts.append(stdout.decode("utf-8", errors="replace"))
-
-            if stderr:
-                stderr_text = stderr.decode("utf-8", errors="replace")
-                if stderr_text.strip():
-                    output_parts.append(f"STDERR:\n{stderr_text}")
-
-            output_parts.append(f"\nExit code: {process.returncode}")
-
-            result = "\n".join(output_parts) if output_parts else "(no output)"
-
-            max_len = self._MAX_OUTPUT
-            if len(result) > max_len:
-                half = max_len // 2
-                result = (
-                    result[:half]
-                    + f"\n\n... ({len(result) - max_len:,} chars truncated) ...\n\n"
-                    + result[-half:]
-                )
-
-            return result
-
-        except Exception as e:
-            return f"Error executing command: {str(e)}"
 
     @staticmethod
     async def _spawn(
         command: str, cwd: str, env: dict[str, str],
+        shell_program: str | None = None,
+        login: bool = True,
     ) -> asyncio.subprocess.Process:
         """Launch *command* in a platform-appropriate shell."""
         if _IS_WINDOWS:
@@ -272,9 +412,13 @@ class ExecTool(Tool):
                 cwd=cwd,
                 env=env,
             )
-        bash = shutil.which("bash") or "/bin/bash"
+        shell_program = shell_program or shutil.which("bash") or "/bin/bash"
+        args = [shell_program]
+        if login and Path(shell_program).name in {"bash", "zsh"}:
+            args.append("-l")
+        args.extend(["-c", command])
         return await asyncio.create_subprocess_exec(
-            bash, "-l", "-c", command,
+            *args,
             stdin=asyncio.subprocess.DEVNULL,
             stdout=asyncio.subprocess.PIPE,
             stderr=asyncio.subprocess.PIPE,
@@ -282,6 +426,31 @@ class ExecTool(Tool):
             env=env,
         )
 
+    @staticmethod
+    def _resolve_shell(shell: str | None) -> tuple[str | None, str | None]:
+        if not shell:
+            return None, None
+        if _IS_WINDOWS:
+            return None, "Error: shell parameter is not supported on Windows"
+        if "\0" in shell or "\n" in shell or "\r" in shell:
+            return None, "Error: shell contains invalid characters"
+        allowed = {"sh", "bash", "zsh"}
+        path = Path(shell).expanduser()
+        if path.is_absolute():
+            if path.name not in allowed:
+                return None, f"Error: unsupported shell {shell!r}. Allowed: bash, sh, zsh"
+            if not path.is_file() or not os.access(path, os.X_OK):
+                return None, f"Error: shell is not executable: {shell}"
+            return str(path), None
+        if "/" in shell or "\\" in shell:
+            return None, "Error: shell must be a shell name or absolute path"
+        if shell not in allowed:
+            return None, f"Error: unsupported shell {shell!r}. Allowed: bash, sh, zsh"
+        resolved = shutil.which(shell)
+        if not resolved:
+            return None, f"Error: shell not found: {shell}"
+        return resolved, None
+
     @staticmethod
     async def _kill_process(process: asyncio.subprocess.Process) -> None:
         """Kill a subprocess and reap it to prevent zombies."""

nanobot/providers/openai_compat_provider.py

@@ -11,6 +11,7 @@ import secrets
 import string
 import time
 import uuid
+from collections import deque
 from collections.abc import Awaitable, Callable
 from ipaddress import ip_address
 from typing import TYPE_CHECKING, Any
@@ -463,6 +464,7 @@ class OpenAICompatProvider(LLMProvider):
         """Strip non-standard keys, normalize tool_call IDs."""
         sanitized = LLMProvider._sanitize_request_messages(messages, _ALLOWED_MSG_KEYS)
         id_map: dict[str, str] = {}
+        pending_tool_ids: dict[str, deque[str]] = {}
         force_string_content = bool(self._spec and self._spec.name == "deepseek")
 
         def map_id(value: Any) -> Any:
@@ -470,15 +472,49 @@ class OpenAICompatProvider(LLMProvider):
                 return value
             return id_map.setdefault(value, self._normalize_tool_call_id(value))
 
+        def unique_tool_id(value: Any, used_ids: set[str], idx: int) -> str:
+            if isinstance(value, str) and value:
+                base = map_id(value)
+            else:
+                base = _short_tool_id()
+            if not isinstance(base, str) or not base:
+                base = _short_tool_id()
+            if base not in used_ids:
+                return base
+            seed = value if isinstance(value, str) and value else base
+            salt = 1
+            while True:
+                candidate = self._normalize_tool_call_id(f"{seed}:{idx}:{salt}")
+                if isinstance(candidate, str) and candidate not in used_ids:
+                    return candidate
+                salt += 1
+
+        def map_tool_result_id(value: Any) -> Any:
+            if not isinstance(value, str):
+                return value
+            queue = pending_tool_ids.get(value)
+            if queue:
+                mapped = queue.popleft()
+                if not queue:
+                    pending_tool_ids.pop(value, None)
+                return mapped
+            return map_id(value)
+
         for clean in sanitized:
             if isinstance(clean.get("tool_calls"), list):
                 normalized = []
-                for tc in clean["tool_calls"]:
+                used_ids: set[str] = set()
+                for idx, tc in enumerate(clean["tool_calls"]):
                     if not isinstance(tc, dict):
                         normalized.append(tc)
                         continue
                     tc_clean = dict(tc)
-                    tc_clean["id"] = map_id(tc_clean.get("id"))
+                    raw_id = tc_clean.get("id")
+                    mapped_id = unique_tool_id(raw_id, used_ids, idx)
+                    tc_clean["id"] = mapped_id
+                    used_ids.add(mapped_id)
+                    if isinstance(raw_id, str) and raw_id:
+                        pending_tool_ids.setdefault(raw_id, deque()).append(mapped_id)
                     function = tc_clean.get("function")
                     if isinstance(function, dict):
                         function_clean = dict(function)
@@ -496,7 +532,7 @@ class OpenAICompatProvider(LLMProvider):
                     # that mix non-empty content with tool_calls.
                     clean["content"] = None
             if "tool_call_id" in clean and clean["tool_call_id"]:
-                clean["tool_call_id"] = map_id(clean["tool_call_id"])
+                clean["tool_call_id"] = map_tool_result_id(clean["tool_call_id"])
             if (
                 force_string_content
                 and not (clean.get("role") == "assistant" and clean.get("tool_calls"))

nanobot/templates/AGENTS.md

@@ -1,5 +1,9 @@
 # Agent Instructions
 
+## Workspace Guidance
+
+Use this file for project-specific preferences, recurring workflow conventions, and instructions you want the agent to remember for this workspace. Keep durable facts about the user in `USER.md`, personality/style guidance in `SOUL.md`, and long-term memory in `memory/MEMORY.md`.
+
 ## Scheduled Reminders
 
 Before scheduling reminders, check available skills and follow skill guidance first.
@@ -10,10 +14,10 @@ Get USER_ID and CHANNEL from the current session (e.g., `8281248569` and `telegr
 
 ## Heartbeat Tasks
 
-`HEARTBEAT.md` is checked on the configured heartbeat interval. Use file tools to manage periodic tasks:
+`HEARTBEAT.md` is checked on the configured heartbeat interval. Use file tools to manage periodic tasks.
 
-- **Add**: `edit_file` to append new tasks
+- Use `apply_patch` for normal task-list updates, especially when adding, removing, or changing multiple lines.
-- **Remove**: `edit_file` to delete completed tasks
+- Use `edit_file` only for small exact replacements copied from the current `HEARTBEAT.md`.
-- **Rewrite**: `write_file` to replace all tasks
+- Use `write_file` for first creation or intentional full-file rewrites.
 
 When the user asks for a recurring/periodic task, update `HEARTBEAT.md` instead of creating a one-time cron reminder.

nanobot/templates/TOOLS.md

@@ -1,28 +0,0 @@
-# Tool Usage Notes
-
-Tool signatures are provided automatically via function calling.
-This file documents non-obvious constraints and usage patterns.
-
-## exec — Safety Limits
-
-- Commands have a configurable timeout (default 60s)
-- Dangerous commands are blocked (rm -rf, format, dd, shutdown, etc.)
-- Output is truncated at 10,000 characters
-- `restrictToWorkspace` config can limit file access to the workspace
-
-## grep — Content Search
-
-- Use `grep` to search file contents inside the workspace
-- Default behavior returns only matching file paths (`output_mode="files_with_matches"`)
-- Supports optional `glob` filtering (e.g. `glob="*.py"`) plus `context_before` / `context_after`
-- Supports `type="py"`, `type="ts"`, `type="md"` and similar shorthand filters
-- Use `fixed_strings=true` for literal keywords containing regex characters
-- Use `output_mode="files_with_matches"` to get only matching file paths
-- Use `output_mode="count"` to size a search before reading full matches
-- Use `head_limit` and `offset` to page across results
-- Prefer this over `exec` for code and history searches
-- Binary or oversized files may be skipped to keep results readable
-
-## cron — Scheduled Reminders
-
-- Please refer to cron skill for usage.

nanobot/templates/agent/tool_contract.md

@@ -0,0 +1,60 @@
+# Tool Usage Notes
+
+Tool signatures are provided automatically via function calling. This section
+documents the general tool contract and non-obvious usage patterns.
+
+## General Tool Contract
+
+- Use the narrowest structured tool that directly matches the task.
+- Use read-only discovery before writes when state is uncertain.
+- Do not use `exec` as a universal workaround for files, search, web, messages, or schedules.
+- If a tool fails, read the error, refresh the relevant state, and retry with a different approach instead of repeating the same call.
+- After meaningful changes, verify with the smallest reliable check: re-read changed state, run targeted tests, or inspect command output.
+- Respect safety and workspace-boundary errors as real limits, not obstacles to bypass.
+
+## Discovery and Reading
+
+- Use `find_files` or `list_dir` to locate workspace paths before `read_file` when a path is uncertain.
+- Use `grep` for content search inside the workspace; prefer it over shell grep for ordinary searches.
+- `grep` defaults to `output_mode="files_with_matches"`; use `output_mode="content"` for matching lines with context.
+- Use `fixed_strings=true` for literal keywords containing regex characters.
+- Use `output_mode="count"` to size a broad search before reading full matches.
+- Use `head_limit` and `offset` to page across large result sets.
+- Binary or oversized files may be skipped to keep results readable.
+
+## File and Coding Workflows
+
+- For code or config changes, the default loop is: locate (`find_files`/`grep`), inspect (`read_file`), edit (`apply_patch`), then verify (`exec` or re-read).
+- Use `apply_patch` as the default code editing tool, especially for multi-file changes, structural edits, generated code, moves, adds, or deletes.
+- Use `apply_patch dry_run=true` when the patch is uncertain and you want validation plus a change summary before writing.
+- Use `edit_file` only for small exact replacements in one file, with `old_text` copied from `read_file`; add `occurrence`, `line_hint`, or `expected_replacements` when ambiguity matters.
+- Use `write_file` for new files or intentional full-file rewrites, not routine partial edits.
+- If `apply_patch` or `edit_file` fails, re-read with `force=true`, narrow the context, and try a smaller patch rather than switching to shell `sed` or `echo`.
+
+## Process Execution
+
+- Use `exec` for tests, builds, package commands, git commands, and other process execution.
+- Prefer dedicated file/search tools over `cat`, shell `find`, shell `grep`, `sed`, or `echo` for ordinary workspace inspection and edits.
+- Use non-interactive flags such as `-y` or `--yes` when available.
+- Commands have a configurable timeout (default 60s), dangerous commands are blocked, and output is truncated.
+- For long-running or interactive commands, pass `yield_time_ms`; if the process keeps running, continue with `write_stdin`.
+- Use `write_stdin` to poll, provide stdin, close stdin, wait for expected output with `wait_for`, or terminate an existing exec session.
+- Use `list_exec_sessions` to recover active session IDs after context shifts.
+
+## Web and External Information
+
+- Use web tools when the user asks for current information, a specific URL, or information likely to have changed.
+- Use `web_search` to find sources and `web_fetch` for a specific page or result that needs closer reading.
+- Do not invent freshness-sensitive facts when tools can verify them.
+
+## Messaging and Media
+
+- Use `message` to send content or local media to the user/channel.
+- `read_file` only reads content for your analysis; it does not deliver a file to the user.
+- When sending an existing local file, attach it through the message/media mechanism instead of pasting file contents unless the user asked for text.
+
+## Scheduling and Background Work
+
+- Use `cron` for scheduled reminders or recurring jobs; do not run `nanobot cron` through `exec`.
+- For heartbeat tasks, update `HEARTBEAT.md` according to the agent instructions.
+- Do not write reminders only to memory files when the user expects an actual notification.

nanobot/utils/file_edit_events.py

@@ -3,14 +3,13 @@
 from __future__ import annotations
 
 import difflib
-import json
 import re
 import time
 from dataclasses import dataclass, field
 from pathlib import Path
 from typing import Any, Awaitable, Callable
 
-TRACKED_FILE_EDIT_TOOLS = frozenset({"write_file", "edit_file", "notebook_edit"})
+TRACKED_FILE_EDIT_TOOLS = frozenset({"write_file", "edit_file", "apply_patch"})
 _MAX_SNAPSHOT_BYTES = 2 * 1024 * 1024
 _LIVE_EMIT_INTERVAL_S = 0.18
 _LIVE_EMIT_LINE_STEP = 24
@@ -153,19 +152,110 @@ def prepare_file_edit_tracker(
     workspace: Path | None,
     params: dict[str, Any] | None,
 ) -> FileEditTracker | None:
+    trackers = prepare_file_edit_trackers(
+        call_id=call_id,
+        tool_name=tool_name,
+        tool=tool,
+        workspace=workspace,
+        params=params,
+    )
+    return trackers[0] if trackers else None
+
+
+def prepare_file_edit_trackers(
+    *,
+    call_id: str,
+    tool_name: str,
+    tool: Any,
+    workspace: Path | None,
+    params: dict[str, Any] | None,
+) -> list[FileEditTracker]:
     if not is_file_edit_tool(tool_name):
-        return None
+        return []
-    path = resolve_file_edit_path(tool, workspace, params)
+    paths = resolve_file_edit_paths(tool_name, tool, workspace, params)
-    if path is None:
+    trackers: list[FileEditTracker] = []
-        return None
+    seen: set[Path] = set()
+    for path in paths:
+        try:
+            resolved = path.resolve()
+        except Exception:
+            resolved = path
+        if resolved in seen:
+            continue
+        seen.add(resolved)
         before = read_file_snapshot(path)
-    return FileEditTracker(
+        trackers.append(FileEditTracker(
             call_id=str(call_id or ""),
             tool=tool_name,
             path=path,
             display_path=display_file_edit_path(path, workspace),
             before=before,
-    )
+        ))
+    return trackers
+
+
+def resolve_file_edit_paths(
+    tool_name: str,
+    tool: Any,
+    workspace: Path | None,
+    params: dict[str, Any] | None,
+) -> list[Path]:
+    if tool_name == "apply_patch":
+        return _resolve_apply_patch_paths(tool, workspace, params)
+    path = resolve_file_edit_path(tool, workspace, params)
+    if path is None:
+        return []
+    return [path]
+
+
+def _resolve_apply_patch_paths(
+    tool: Any,
+    workspace: Path | None,
+    params: dict[str, Any] | None,
+) -> list[Path]:
+    if not isinstance(params, dict):
+        return []
+    patch = params.get("patch")
+    if not isinstance(patch, str) or not patch.strip():
+        return []
+    if params.get("dry_run") is True:
+        return []
+    try:
+        from nanobot.agent.tools.apply_patch import _parse_patch
+
+        ops = _parse_patch(patch)
+    except Exception:
+        return []
+
+    resolved: list[Path] = []
+    for op in ops:
+        for raw_path in (op.path, op.new_path):
+            if not raw_path:
+                continue
+            path = _resolve_raw_file_edit_path(tool, workspace, raw_path)
+            if path is not None:
+                resolved.append(path)
+    return resolved
+
+
+def _resolve_raw_file_edit_path(
+    tool: Any,
+    workspace: Path | None,
+    raw_path: str,
+) -> Path | None:
+    resolver = getattr(tool, "_resolve", None)
+    if callable(resolver):
+        try:
+            resolved = resolver(raw_path)
+            if isinstance(resolved, Path):
+                return resolved
+            if resolved:
+                return Path(resolved)
+        except Exception:
+            return None
+    if workspace is None:
+        return Path(raw_path).expanduser().resolve()
+    return (workspace / raw_path).expanduser().resolve()
 
 
 def build_file_edit_start_event(
@@ -303,6 +393,9 @@ class StreamingFileEditTracker:
             self._states[key] = state
 
         state.apply_delta(payload)
+        if state.name == "apply_patch":
+            await self._update_apply_patch(state)
+            return
         if state.name not in {"write_file", "edit_file"}:
             return
         if state.path is None:
@@ -342,10 +435,62 @@ class StreamingFileEditTracker:
             deleted=deleted,
         )])
 
+    async def _update_apply_patch(self, state: _StreamingFileEditState) -> None:
+        if _json_bool_true(state.arguments, "dry_run"):
+            return
+        patch = _extract_json_string_prefix(state.arguments, "patch")
+        if not patch:
+            return
+        tool = self._tools.get("apply_patch") if hasattr(self._tools, "get") else None
+        events: list[dict[str, Any]] = []
+        now = time.monotonic()
+        for raw_path, added, deleted, delete_file in _streaming_apply_patch_stats(patch):
+            path = _resolve_raw_file_edit_path(tool, self._workspace, raw_path)
+            if path is None:
+                continue
+            file_state = state.patch_files.get(raw_path)
+            if file_state is None:
+                tracker = FileEditTracker(
+                    call_id=state.call_id or state.key,
+                    tool="apply_patch",
+                    path=path,
+                    display_path=display_file_edit_path(path, self._workspace),
+                    before=read_file_snapshot(path),
+                )
+                file_state = _StreamingPatchFileState(tracker=tracker)
+                state.patch_files[raw_path] = file_state
+            if delete_file and added == 0 and deleted == 0 and file_state.tracker.before.countable:
+                deleted = _text_line_count(file_state.tracker.before.text or "")
+            if not file_state.should_emit(added, deleted, now):
+                continue
+            file_state.mark_emitted(added, deleted, now)
+            events.append(build_file_edit_live_event(
+                file_state.tracker,
+                added=added,
+                deleted=deleted,
+            ))
+        if events:
+            await self._emit(events)
+
     async def flush(self) -> None:
         events: list[dict[str, Any]] = []
         now = time.monotonic()
         for state in self._states.values():
+            for file_state in state.patch_files.values():
+                added, deleted = file_state.last_added, file_state.last_deleted
+                if not file_state.emitted_once:
+                    continue
+                if (
+                    file_state.last_emitted_added == added
+                    and file_state.last_emitted_deleted == deleted
+                ):
+                    continue
+                file_state.mark_emitted(added, deleted, now)
+                events.append(build_file_edit_live_event(
+                    file_state.tracker,
+                    added=added,
+                    deleted=deleted,
+                ))
             if state.tracker is None:
                 continue
             added, deleted = state.live_diff_counts()
@@ -390,6 +535,10 @@ class StreamingFileEditTracker:
         """Mark streamed edits as failed when no final tool call will run."""
         events: list[dict[str, Any]] = []
         for state in self._states.values():
+            for file_state in state.patch_files.values():
+                if any(state.matches_final_tool_call(tool_call) for tool_call in final_tool_calls):
+                    continue
+                events.append(build_file_edit_error_event(file_state.tracker, error))
             if state.tracker is None:
                 continue
             if any(state.matches_final_tool_call(tool_call) for tool_call in final_tool_calls):
@@ -493,6 +642,39 @@ class _StreamingJsonStringField:
             self.last_char_cr = False
 
 
+@dataclass(slots=True)
+class _StreamingPatchFileState:
+    tracker: FileEditTracker
+    emitted_once: bool = False
+    last_emitted_added: int = -1
+    last_emitted_deleted: int = -1
+    last_emit_at: float = 0.0
+    last_added: int = 0
+    last_deleted: int = 0
+
+    def should_emit(self, added: int, deleted: int, now: float) -> bool:
+        self.last_added = added
+        self.last_deleted = deleted
+        if not self.emitted_once:
+            return True
+        if added == self.last_emitted_added and deleted == self.last_emitted_deleted:
+            return False
+        if max(
+            abs(added - self.last_emitted_added),
+            abs(deleted - self.last_emitted_deleted),
+        ) >= _LIVE_EMIT_LINE_STEP:
+            return True
+        return now - self.last_emit_at >= _LIVE_EMIT_INTERVAL_S
+
+    def mark_emitted(self, added: int, deleted: int, now: float) -> None:
+        self.emitted_once = True
+        self.last_added = added
+        self.last_deleted = deleted
+        self.last_emitted_added = added
+        self.last_emitted_deleted = deleted
+        self.last_emit_at = now
+
+
 @dataclass(slots=True)
 class _StreamingFileEditState:
     key: str
@@ -510,6 +692,7 @@ class _StreamingFileEditState:
     new_text: _StreamingJsonStringField = field(
         default_factory=lambda: _StreamingJsonStringField("new_text")
     )
+    patch_files: dict[str, _StreamingPatchFileState] = field(default_factory=dict)
     emitted_once: bool = False
     last_emitted_added: int = -1
     last_emitted_deleted: int = -1
@@ -532,6 +715,7 @@ class _StreamingFileEditState:
             self.content.reset()
             self.old_text.reset()
             self.new_text.reset()
+            self.patch_files.clear()
             return
         delta = payload.get("arguments_delta")
         if isinstance(delta, str) and delta:
@@ -591,6 +775,13 @@ class _StreamingFileEditState:
         name = getattr(tool_call, "name", None)
         if name != self.name:
             return False
+        if self.name == "apply_patch":
+            arguments = getattr(tool_call, "arguments", None)
+            if not isinstance(arguments, dict):
+                return False
+            patch = arguments.get("patch")
+            streamed_patch = _extract_complete_json_string(self.arguments, "patch")
+            return isinstance(patch, str) and streamed_patch == patch
         arguments = getattr(tool_call, "arguments", None)
         if not isinstance(arguments, dict):
             return False
@@ -613,6 +804,110 @@ def _stream_key(payload: dict[str, Any]) -> str:
     return ""
 
 
+def _json_bool_true(source: str, key: str) -> bool:
+    return re.search(rf'"{re.escape(key)}"\s*:\s*true\b', source) is not None
+
+
+def _extract_json_string_prefix(source: str, key: str) -> str | None:
+    match = re.search(rf'"{re.escape(key)}"\s*:\s*"', source)
+    if match is None:
+        return None
+    out: list[str] = []
+    i = match.end()
+    escape = False
+    while i < len(source):
+        ch = source[i]
+        if escape:
+            escape = False
+            if ch == "n":
+                out.append("\n")
+            elif ch == "r":
+                out.append("\r")
+            elif ch == "t":
+                out.append("\t")
+            elif ch == "u":
+                digits = source[i + 1:i + 5]
+                if len(digits) < 4:
+                    break
+                try:
+                    out.append(chr(int(digits, 16)))
+                except ValueError:
+                    break
+                i += 4
+            else:
+                out.append(ch)
+            i += 1
+            continue
+        if ch == "\\":
+            escape = True
+            i += 1
+            continue
+        if ch == '"':
+            return "".join(out)
+        out.append(ch)
+        i += 1
+    return "".join(out)
+
+
+def _streaming_apply_patch_stats(patch: str) -> list[tuple[str, int, int, bool]]:
+    stats: dict[str, list[Any]] = {}
+    order: list[str] = []
+    current: str | None = None
+
+    def ensure(path: str, *, delete_file: bool = False) -> list[Any]:
+        if path not in stats:
+            stats[path] = [0, 0, False]
+            order.append(path)
+        if delete_file:
+            stats[path][2] = True
+        return stats[path]
+
+    lines = patch.splitlines()
+    tail = ""
+    if patch and not patch.endswith(("\n", "\r")) and lines:
+        tail = lines.pop()
+
+    for line in lines:
+        if line.startswith("*** Add File: "):
+            current = line[len("*** Add File: "):].strip()
+            if current:
+                ensure(current)
+            continue
+        if line.startswith("*** Update File: "):
+            current = line[len("*** Update File: "):].strip()
+            if current:
+                ensure(current)
+            continue
+        if line.startswith("*** Delete File: "):
+            current = line[len("*** Delete File: "):].strip()
+            if current:
+                ensure(current, delete_file=True)
+            continue
+        if line.startswith("*** Move to: "):
+            moved = line[len("*** Move to: "):].strip()
+            if moved:
+                current = moved
+                ensure(current)
+            continue
+        if line.startswith("*** "):
+            current = None
+            continue
+        if not current:
+            continue
+        if line.startswith("+") and not line.startswith("+++"):
+            ensure(current)[0] += 1
+        elif line.startswith("-") and not line.startswith("---"):
+            ensure(current)[1] += 1
+
+    if current and tail:
+        if tail.startswith("+") and not tail.startswith("+++"):
+            ensure(current)[0] += 1
+        elif tail.startswith("-") and not tail.startswith("---"):
+            ensure(current)[1] += 1
+
+    return [(path, int(stats[path][0]), int(stats[path][1]), bool(stats[path][2])) for path in order]
+
+
 def _extract_complete_json_string(source: str, key: str) -> str | None:
     match = re.search(rf'"{re.escape(key)}"\s*:\s*"', source)
     if match is None:
@@ -705,77 +1000,4 @@ def _predict_after_text(
                 return before_text.replace(old_text, new_text)
             return before_text.replace(old_text, new_text, 1)
         return None
-    if tool_name == "notebook_edit":
-        return _predict_notebook_after_text(params, before_text)
     return None
-
-
-def _predict_notebook_after_text(params: dict[str, Any], before_text: str) -> str | None:
-    try:
-        nb = json.loads(before_text) if before_text.strip() else _empty_notebook()
-    except Exception:
-        return None
-    cells = nb.get("cells")
-    if not isinstance(cells, list):
-        return None
-    try:
-        cell_index = int(params.get("cell_index", 0))
-    except (TypeError, ValueError):
-        return None
-    new_source = params.get("new_source")
-    source = new_source if isinstance(new_source, str) else ""
-    cell_type = (
-        params.get("cell_type") if params.get("cell_type") in ("code", "markdown") else "code"
-    )
-    mode = (
-        params.get("edit_mode")
-        if params.get("edit_mode") in ("replace", "insert", "delete")
-        else "replace"
-    )
-    if mode == "delete":
-        if 0 <= cell_index < len(cells):
-            cells.pop(cell_index)
-        else:
-            return None
-    elif mode == "insert":
-        insert_at = min(max(cell_index + 1, 0), len(cells))
-        cells.insert(insert_at, _new_notebook_cell(source, str(cell_type)))
-    else:
-        if not (0 <= cell_index < len(cells)):
-            return None
-        cell = cells[cell_index]
-        if not isinstance(cell, dict):
-            return None
-        cell["source"] = source
-        cell["cell_type"] = cell_type
-        if cell_type == "code":
-            cell.setdefault("outputs", [])
-            cell.setdefault("execution_count", None)
-        else:
-            cell.pop("outputs", None)
-            cell.pop("execution_count", None)
-    nb["cells"] = cells
-    try:
-        return json.dumps(nb, indent=1, ensure_ascii=False)
-    except Exception:
-        return None
-
-
-def _empty_notebook() -> dict[str, Any]:
-    return {
-        "nbformat": 4,
-        "nbformat_minor": 5,
-        "metadata": {
-            "kernelspec": {"display_name": "Python 3", "language": "python", "name": "python3"},
-            "language_info": {"name": "python"},
-        },
-        "cells": [],
-    }
-
-
-def _new_notebook_cell(source: str, cell_type: str) -> dict[str, Any]:
-    cell: dict[str, Any] = {"cell_type": cell_type, "source": source, "metadata": {}}
-    if cell_type == "code":
-        cell["outputs"] = []
-        cell["execution_count"] = None
-    return cell

nanobot/utils/helpers.py

@@ -576,7 +576,7 @@ def build_status_content(
 
 
 def sync_workspace_templates(workspace: Path, silent: bool = False) -> list[str]:
-    """Sync bundled templates to workspace. Only creates missing files."""
+    """Sync bundled templates to workspace. Creates missing files without overwriting user files."""
     from importlib.resources import files as pkg_files
 
     try:
@@ -589,10 +589,11 @@ def sync_workspace_templates(workspace: Path, silent: bool = False) -> list[str]
     added: list[str] = []
 
     def _write(src, dest: Path):
+        content = src.read_text(encoding="utf-8") if src else ""
         if dest.exists():
             return
         dest.parent.mkdir(parents=True, exist_ok=True)
-        dest.write_text(src.read_text(encoding="utf-8") if src else "", encoding="utf-8")
+        dest.write_text(content, encoding="utf-8")
         added.append(str(dest.relative_to(workspace)))
 
     for item in tpl.iterdir():

nanobot/utils/tool_hints.py

@@ -11,8 +11,10 @@ _TOOL_FORMATS: dict[str, tuple[list[str], str, bool, bool]] = {
     "read_file":  (["path", "file_path"],              "read {}",     True,  False),
     "write_file": (["path", "file_path"],              "write {}",    True,  False),
     "edit":       (["file_path", "path"],              "edit {}",     True,  False),
+    "find_files": (["query", "glob", "path"],           "find {}",     False, False),
     "grep":       (["pattern"],                        'grep "{}"',   False, False),
     "exec":       (["command"],                        "$ {}",        False, True),
+    "list_exec_sessions": ([],                          "exec sessions", False, False),
     "web_search": (["query"],                          'search "{}"', False, False),
     "web_fetch":  (["url"],                            "fetch {}",    True,  False),
     "list_dir":   (["path"],                           "ls {}",       True,  False),
@@ -81,6 +83,8 @@ def _extract_arg(tc, key_args: list[str]) -> str | None:
 
 def _fmt_known(tc, fmt: tuple, max_length: int = 40) -> str:
     """Format a registered tool using its template."""
+    if not fmt[0] and "{}" not in fmt[1]:
+        return fmt[1]
     val = _extract_arg(tc, fmt[0])
     if val is None:
         return tc.name

tests/agent/test_context_builder.py

@@ -139,6 +139,13 @@ class TestLoadBootstrapFiles:
         for name in ContextBuilder.BOOTSTRAP_FILES:
             assert f"## {name}" in result
 
+    def test_legacy_tools_md_is_not_bootstrapped(self, tmp_path):
+        (tmp_path / "TOOLS.md").write_text("workspace tool notes", encoding="utf-8")
+        builder = _builder(tmp_path)
+        result = builder._load_bootstrap_files()
+        assert "TOOLS.md" not in result
+        assert "workspace tool notes" not in result
+
     def test_utf8_content(self, tmp_path):
         (tmp_path / "AGENTS.md").write_text("用中文回复", encoding="utf-8")
         builder = _builder(tmp_path)
@@ -171,6 +178,37 @@ class TestIsTemplateContent:
         assert ContextBuilder._is_template_content("totally different", "memory/MEMORY.md") is False
 
 
+# ---------------------------------------------------------------------------
+# Bundled bootstrap templates
+# ---------------------------------------------------------------------------
+
+
+class TestBundledToolContract:
+    def test_tool_contract_balances_general_and_coding_workflows(self):
+        from importlib.resources import files as pkg_files
+
+        tpl = pkg_files("nanobot") / "templates" / "agent" / "tool_contract.md"
+        content = tpl.read_text(encoding="utf-8")
+
+        assert "## General Tool Contract" in content
+        assert "Use the narrowest structured tool" in content
+        assert "Do not use `exec` as a universal workaround" in content
+        assert "## File and Coding Workflows" in content
+        assert "apply_patch" in content
+        assert "## Web and External Information" in content
+        assert "## Messaging and Media" in content
+        assert "## Scheduling and Background Work" in content
+        assert "pure coding" not in content.lower()
+
+    def test_tool_contract_is_injected_without_workspace_file(self, tmp_path):
+        builder = _builder(tmp_path)
+        prompt = builder.build_system_prompt()
+
+        assert "# Tool Usage Notes" in prompt
+        assert "## General Tool Contract" in prompt
+        assert "Do not use `exec` as a universal workaround" in prompt
+
+
 # ---------------------------------------------------------------------------
 # _build_user_content
 # ---------------------------------------------------------------------------

tests/agent/test_onboard_logic.py

@@ -346,6 +346,26 @@ class TestSyncWorkspaceTemplates:
         content = (workspace / "AGENTS.md").read_text()
         assert content == "existing content"
 
+    def test_does_not_create_tools_md(self, tmp_path):
+        """Tool contract is injected internally, not copied into user workspaces."""
+        workspace = tmp_path / "workspace"
+
+        added = sync_workspace_templates(workspace, silent=True)
+
+        assert "TOOLS.md" not in added
+        assert not (workspace / "TOOLS.md").exists()
+
+    def test_preserves_existing_tools_md_without_overwriting(self, tmp_path):
+        """Legacy user workspaces may have TOOLS.md; sync should leave it untouched."""
+        workspace = tmp_path / "workspace"
+        workspace.mkdir(parents=True)
+        tools_path = workspace / "TOOLS.md"
+        tools_path.write_text("custom tool notes", encoding="utf-8")
+
+        sync_workspace_templates(workspace, silent=True)
+
+        assert tools_path.read_text(encoding="utf-8") == "custom tool notes"
+
     def test_creates_memory_directory(self, tmp_path):
         """Should create memory directory structure."""
         workspace = tmp_path / "workspace"

tests/providers/test_litellm_kwargs.py

@@ -1007,6 +1007,41 @@ def test_openai_compat_keeps_tool_calls_after_consecutive_assistant_messages() -
     assert sanitized[2]["tool_call_id"] == "3ec83c30d"
 
 
+def test_openai_compat_deduplicates_duplicate_tool_call_ids_in_history() -> None:
+    with patch("nanobot.providers.openai_compat_provider.AsyncOpenAI"):
+        provider = OpenAICompatProvider()
+
+    sanitized = provider._sanitize_messages([
+        {"role": "user", "content": "check both files"},
+        {
+            "role": "assistant",
+            "content": "",
+            "tool_calls": [
+                {
+                    "id": "ab1b45c2a",
+                    "type": "function",
+                    "function": {"name": "read_file", "arguments": '{"path":"a.txt"}'},
+                },
+                {
+                    "id": "ab1b45c2a",
+                    "type": "function",
+                    "function": {"name": "read_file", "arguments": '{"path":"b.txt"}'},
+                },
+            ],
+        },
+        {"role": "tool", "tool_call_id": "ab1b45c2a", "name": "read_file", "content": "a"},
+        {"role": "tool", "tool_call_id": "ab1b45c2a", "name": "read_file", "content": "b"},
+        {"role": "user", "content": "continue"},
+    ])
+
+    tool_call_ids = [tc["id"] for tc in sanitized[1]["tool_calls"]]
+    tool_result_ids = [sanitized[2]["tool_call_id"], sanitized[3]["tool_call_id"]]
+
+    assert tool_call_ids[0] == "ab1b45c2a"
+    assert len(tool_call_ids) == len(set(tool_call_ids)) == 2
+    assert tool_result_ids == tool_call_ids
+
+
 def test_openai_compat_stringifies_dict_tool_arguments() -> None:
     with patch("nanobot.providers.openai_compat_provider.AsyncOpenAI"):
         provider = OpenAICompatProvider()

tests/tools/test_apply_patch_tool.py

@@ -0,0 +1,287 @@
+from __future__ import annotations
+
+import asyncio
+
+from nanobot.agent.tools.apply_patch import ApplyPatchTool
+
+
+def test_apply_patch_adds_file(tmp_path):
+    tool = ApplyPatchTool(workspace=tmp_path)
+
+    result = asyncio.run(tool.execute(
+        patch="""*** Begin Patch
+*** Add File: hello.txt
++Hello
++world
+*** End Patch
+"""
+    ))
+
+    assert "Patch applied" in result
+    assert (tmp_path / "hello.txt").read_text() == "Hello\nworld\n"
+
+
+def test_apply_patch_updates_multiple_hunks(tmp_path):
+    target = tmp_path / "multi.txt"
+    target.write_text("line1\nline2\nline3\nline4\n")
+    tool = ApplyPatchTool(workspace=tmp_path)
+
+    result = asyncio.run(tool.execute(
+        patch="""*** Begin Patch
+*** Update File: multi.txt
+@@
+-line2
++changed2
+@@
+-line4
++changed4
+*** End Patch
+"""
+    ))
+
+    assert "update multi.txt" in result
+    assert "(+2/-2)" in result
+    assert target.read_text() == "line1\nchanged2\nline3\nchanged4\n"
+
+
+def test_apply_patch_dry_run_validates_without_writing(tmp_path):
+    target = tmp_path / "dry.txt"
+    target.write_text("before\n")
+    tool = ApplyPatchTool(workspace=tmp_path)
+
+    result = asyncio.run(tool.execute(
+        patch="""*** Begin Patch
+*** Update File: dry.txt
+@@
+-before
++after
+*** Add File: added.txt
++new
+*** End Patch
+""",
+        dry_run=True,
+    ))
+
+    assert "Patch dry-run succeeded" in result
+    assert "- update dry.txt (+1/-1)" in result
+    assert "- add added.txt (+1/-0)" in result
+    assert target.read_text() == "before\n"
+    assert not (tmp_path / "added.txt").exists()
+
+
+def test_apply_patch_applies_repeated_update_sections_sequentially(tmp_path):
+    target = tmp_path / "repeat.txt"
+    target.write_text("one\ntwo\nthree\n")
+    tool = ApplyPatchTool(workspace=tmp_path)
+
+    result = asyncio.run(tool.execute(
+        patch="""*** Begin Patch
+*** Update File: repeat.txt
+@@
+-one
++ONE
+*** Update File: repeat.txt
+@@
+-three
++THREE
+*** End Patch
+"""
+    ))
+
+    assert result.count("update repeat.txt") == 2
+    assert target.read_text() == "ONE\ntwo\nTHREE\n"
+
+
+def test_apply_patch_ignores_standard_no_newline_marker(tmp_path):
+    target = tmp_path / "plain.txt"
+    target.write_text("before")
+    tool = ApplyPatchTool(workspace=tmp_path)
+
+    result = asyncio.run(tool.execute(
+        patch="""*** Begin Patch
+*** Update File: plain.txt
+@@ -1,1 +1,1 @@
+-before
+\\ No newline at end of file
++after
+\\ No newline at end of file
+*** End Patch
+"""
+    ))
+
+    assert "update plain.txt" in result
+    assert target.read_text() == "after\n"
+
+
+def test_apply_patch_rejects_empty_hunk(tmp_path):
+    target = tmp_path / "plain.txt"
+    target.write_text("before\n")
+    tool = ApplyPatchTool(workspace=tmp_path)
+
+    result = asyncio.run(tool.execute(
+        patch="""*** Begin Patch
+*** Update File: plain.txt
+@@
+*** End Patch
+"""
+    ))
+
+    assert "hunk is empty" in result
+    assert target.read_text() == "before\n"
+
+
+def test_apply_patch_uses_unified_diff_line_hint(tmp_path):
+    target = tmp_path / "repeated.txt"
+    target.write_text("target\nmiddle\ntarget\n")
+    tool = ApplyPatchTool(workspace=tmp_path)
+
+    result = asyncio.run(tool.execute(
+        patch="""*** Begin Patch
+*** Update File: repeated.txt
+@@ -3,1 +3,1 @@
+-target
++changed
+*** End Patch
+"""
+    ))
+
+    assert "update repeated.txt" in result
+    assert target.read_text() == "target\nmiddle\nchanged\n"
+
+
+def test_apply_patch_line_hint_does_not_fallback_to_earlier_match(tmp_path):
+    target = tmp_path / "repeated.txt"
+    target.write_text("target\nmiddle\nother\n")
+    tool = ApplyPatchTool(workspace=tmp_path)
+
+    result = asyncio.run(tool.execute(
+        patch="""*** Begin Patch
+*** Update File: repeated.txt
+@@ -3,1 +3,1 @@
+-target
++changed
+*** End Patch
+"""
+    ))
+
+    assert "hunk does not match repeated.txt" in result
+    assert target.read_text() == "target\nmiddle\nother\n"
+
+
+def test_apply_patch_mismatch_reports_best_match(tmp_path):
+    target = tmp_path / "near.txt"
+    target.write_text("alpha\nbeta\ngamma\n")
+    tool = ApplyPatchTool(workspace=tmp_path)
+
+    result = asyncio.run(tool.execute(
+        patch="""*** Begin Patch
+*** Update File: near.txt
+@@ -2,1 +2,1 @@
+-betx
++delta
+*** End Patch
+"""
+    ))
+
+    assert "hunk does not match near.txt" in result
+    assert "Best match" in result
+    assert "line 2" in result
+    assert target.read_text() == "alpha\nbeta\ngamma\n"
+
+
+def test_apply_patch_moves_and_updates_file(tmp_path):
+    source = tmp_path / "old" / "name.txt"
+    source.parent.mkdir()
+    source.write_text("old content\n")
+    tool = ApplyPatchTool(workspace=tmp_path)
+
+    result = asyncio.run(tool.execute(
+        patch="""*** Begin Patch
+*** Update File: old/name.txt
+*** Move to: renamed/dir/name.txt
+@@
+-old content
++new content
+*** End Patch
+"""
+    ))
+
+    assert "move old/name.txt -> renamed/dir/name.txt" in result
+    assert not source.exists()
+    assert (tmp_path / "renamed" / "dir" / "name.txt").read_text() == "new content\n"
+
+
+def test_apply_patch_deletes_file(tmp_path):
+    target = tmp_path / "obsolete.txt"
+    target.write_text("remove me\n")
+    tool = ApplyPatchTool(workspace=tmp_path)
+
+    result = asyncio.run(tool.execute(
+        patch="""*** Begin Patch
+*** Delete File: obsolete.txt
+*** End Patch
+"""
+    ))
+
+    assert "delete obsolete.txt" in result
+    assert not target.exists()
+
+
+def test_apply_patch_rejects_absolute_and_parent_paths(tmp_path):
+    tool = ApplyPatchTool(workspace=tmp_path)
+
+    absolute = asyncio.run(tool.execute(
+        patch="""*** Begin Patch
+*** Add File: /tmp/owned.txt
++nope
+*** End Patch
+"""
+    ))
+    parent = asyncio.run(tool.execute(
+        patch="""*** Begin Patch
+*** Add File: ../owned.txt
++nope
+*** End Patch
+"""
+    ))
+
+    assert "must be relative" in absolute
+    assert "must not contain '..'" in parent
+    assert not (tmp_path.parent / "owned.txt").exists()
+
+
+def test_apply_patch_does_not_overwrite_existing_file_with_add(tmp_path):
+    target = tmp_path / "existing.txt"
+    target.write_text("keep me\n")
+    tool = ApplyPatchTool(workspace=tmp_path)
+
+    result = asyncio.run(tool.execute(
+        patch="""*** Begin Patch
+*** Add File: existing.txt
++replace me
+*** End Patch
+"""
+    ))
+
+    assert "file to add already exists" in result
+    assert target.read_text() == "keep me\n"
+
+
+def test_apply_patch_rolls_back_when_late_operation_fails(tmp_path):
+    first = tmp_path / "first.txt"
+    first.write_text("before\n")
+    tool = ApplyPatchTool(workspace=tmp_path)
+
+    result = asyncio.run(tool.execute(
+        patch="""*** Begin Patch
+*** Update File: first.txt
+@@
+-before
++after
+*** Delete File: missing.txt
+*** End Patch
+"""
+    ))
+
+    assert "file to delete does not exist" in result
+    assert first.read_text() == "before\n"

tests/tools/test_edit_enhancements.py

@@ -1,5 +1,5 @@
 """Tests for EditFileTool enhancements: read-before-edit tracking, path suggestions,
-.ipynb detection, and create-file semantics."""
+notebook JSON editing, and create-file semantics."""
 
 import pytest
 
@@ -108,22 +108,27 @@ class TestEditCreateFile:
 
 
 # ---------------------------------------------------------------------------
-# .ipynb detection
+# .ipynb editing
 # ---------------------------------------------------------------------------
 
-class TestEditIpynbDetection:
+class TestEditIpynbFiles:
-    """edit_file should refuse .ipynb and suggest notebook_edit."""
+    """edit_file edits notebooks as normal JSON files."""
 
     @pytest.fixture()
     def tool(self, tmp_path):
         return EditFileTool(workspace=tmp_path)
 
     @pytest.mark.asyncio
-    async def test_ipynb_rejected_with_suggestion(self, tool, tmp_path):
+    async def test_ipynb_can_be_edited_as_json(self, tool, tmp_path):
         f = tmp_path / "analysis.ipynb"
         f.write_text('{"cells": []}', encoding="utf-8")
-        result = await tool.execute(path=str(f), old_text="x", new_text="y")
+        result = await tool.execute(
-        assert "notebook" in result.lower()
+            path=str(f),
+            old_text='"cells": []',
+            new_text='"cells": [{"cell_type": "markdown", "source": "hi"}]',
+        )
+        assert "Successfully edited" in result
+        assert '"source": "hi"' in f.read_text(encoding="utf-8")
 
 
 # ---------------------------------------------------------------------------

tests/tools/test_exec_platform.py

@@ -162,7 +162,7 @@ class TestPathAppendPlatform:
         captured_cmd = None
         captured_env = {}
 
-        async def capture_spawn(cmd, cwd, env):
+        async def capture_spawn(cmd, cwd, env, shell_program=None, login=True):
             nonlocal captured_cmd
             captured_cmd = cmd
             captured_env.update(env)
@@ -190,7 +190,7 @@ class TestPathAppendPlatform:
 
         captured_env = {}
 
-        async def capture_spawn(cmd, cwd, env):
+        async def capture_spawn(cmd, cwd, env, shell_program=None, login=True):
             captured_env.update(env)
             return mock_proc
 

tests/tools/test_exec_session_tools.py

@@ -0,0 +1,358 @@
+from __future__ import annotations
+
+import asyncio
+import re
+import shlex
+import subprocess
+import sys
+
+from nanobot.agent.tools.shell import ExecTool
+from nanobot.agent.tools.exec_session import ExecSessionManager, ListExecSessionsTool, WriteStdinTool
+
+
+def _python_command(code: str) -> str:
+    if sys.platform == "win32":
+        return f"{subprocess.list2cmdline([sys.executable])} -u -c {subprocess.list2cmdline([code])}"
+    return f"{shlex.quote(sys.executable)} -u -c {shlex.quote(code)}"
+
+
+def _session_id(output: str) -> str:
+    match = re.search(r"session_id:\s*([0-9a-f]+)", output)
+    assert match, output
+    return match.group(1)
+
+
+def test_exec_keeps_one_shot_behavior_without_yield_time_ms(tmp_path):
+    async def run() -> str:
+        tool = ExecTool(working_dir=str(tmp_path), timeout=5)
+        return await tool.execute(command="echo hello")
+
+    result = asyncio.run(run())
+
+    assert "hello" in result
+    assert "Exit code: 0" in result
+    assert "session_id:" not in result
+
+
+def test_exec_accepts_command_aliases(tmp_path):
+    async def run() -> str:
+        tool = ExecTool(working_dir="/")
+        return await tool.execute(cmd="pwd", workdir=str(tmp_path))
+
+    result = asyncio.run(run())
+
+    assert str(tmp_path) in result
+    assert "Exit code: 0" in result
+
+
+def test_exec_returns_completed_session_output_when_yield_time_ms_is_used(tmp_path):
+    async def run() -> str:
+        manager = ExecSessionManager()
+        tool = ExecTool(working_dir=str(tmp_path), timeout=5, session_manager=manager)
+        stdin_tool = WriteStdinTool(manager=manager)
+
+        result = await tool.execute(command="echo hello", yield_time_ms=1000)
+        if "session_id:" in result:
+            sid = _session_id(result)
+            result += "\n" + await stdin_tool.execute(
+                session_id=sid,
+                chars="",
+                yield_time_ms=1000,
+            )
+        return result
+
+    result = asyncio.run(run())
+
+    assert "hello" in result
+    assert "Exit code: 0" in result
+    assert "session_id:" not in result
+
+
+def test_exec_session_accepts_max_output_tokens_alias(tmp_path):
+    async def run() -> str:
+        manager = ExecSessionManager()
+        tool = ExecTool(working_dir=str(tmp_path), timeout=5, session_manager=manager)
+        command = _python_command("print('A' * 2000)")
+        return await tool.execute(
+            command=command,
+            yield_time_ms=1000,
+            max_output_tokens=1000,
+        )
+
+    result = asyncio.run(run())
+
+    assert "chars truncated" in result
+    assert "Exit code: 0" in result
+
+
+def test_exec_one_shot_accepts_max_output_tokens_alias(tmp_path):
+    async def run() -> str:
+        tool = ExecTool(working_dir=str(tmp_path), timeout=5)
+        command = _python_command("print('A' * 2000)")
+        return await tool.execute(command=command, max_output_tokens=1000)
+
+    result = asyncio.run(run())
+
+    assert "chars truncated" in result
+    assert "Exit code: 0" in result
+
+
+def test_exec_accepts_supported_shell_parameter(tmp_path):
+    async def run() -> str:
+        tool = ExecTool(working_dir=str(tmp_path), timeout=5)
+        return await tool.execute(command="echo shell-ok", shell="sh", login=False)
+
+    if sys.platform == "win32":
+        return
+    result = asyncio.run(run())
+
+    assert "shell-ok" in result
+    assert "Exit code: 0" in result
+
+
+def test_exec_rejects_unsupported_shell(tmp_path):
+    async def run() -> str:
+        tool = ExecTool(working_dir=str(tmp_path), timeout=5)
+        return await tool.execute(command="echo no", shell="python")
+
+    if sys.platform == "win32":
+        return
+    result = asyncio.run(run())
+
+    assert "unsupported shell" in result
+
+
+def test_exec_can_continue_with_stdin(tmp_path):
+    async def run() -> tuple[str, str]:
+        manager = ExecSessionManager()
+        exec_tool = ExecTool(working_dir=str(tmp_path), timeout=5, session_manager=manager)
+        stdin_tool = WriteStdinTool(manager=manager)
+        command = _python_command(
+            "import sys; print('ready', flush=True); "
+            "line=sys.stdin.readline(); print('got:' + line.strip(), flush=True)"
+        )
+
+        initial = await exec_tool.execute(command=command, yield_time_ms=500)
+        sid = _session_id(initial)
+        result = await stdin_tool.execute(session_id=sid, chars="ping\n", yield_time_ms=1000)
+        return initial, result
+
+    initial, result = asyncio.run(run())
+    assert "ready" in initial
+    assert "Process running" in initial
+    assert "Elapsed:" in initial
+    assert "got:ping" in result
+    assert "Exit code: 0" in result
+    assert "Elapsed:" in result
+
+
+def test_write_stdin_can_close_stdin(tmp_path):
+    async def run() -> tuple[str, str]:
+        manager = ExecSessionManager()
+        exec_tool = ExecTool(working_dir=str(tmp_path), timeout=5, session_manager=manager)
+        stdin_tool = WriteStdinTool(manager=manager)
+        command = _python_command(
+            "import sys; print('ready', flush=True); "
+            "data=sys.stdin.read(); print('got:' + data, flush=True)"
+        )
+
+        initial = await exec_tool.execute(command=command, yield_time_ms=500)
+        sid = _session_id(initial)
+        result = await stdin_tool.execute(
+            session_id=sid,
+            chars="payload",
+            close_stdin=True,
+            yield_time_ms=1000,
+        )
+        return initial, result
+
+    initial, result = asyncio.run(run())
+    assert "ready" in initial
+    assert "got:payload" in result
+    assert "Stdin closed." in result
+    assert "Exit code: 0" in result
+
+
+def test_write_stdin_can_terminate_session(tmp_path):
+    async def run() -> tuple[str, str]:
+        manager = ExecSessionManager()
+        exec_tool = ExecTool(working_dir=str(tmp_path), timeout=30, session_manager=manager)
+        stdin_tool = WriteStdinTool(manager=manager)
+        command = _python_command(
+            "import time; print('ready', flush=True); time.sleep(30)"
+        )
+
+        initial = await exec_tool.execute(command=command, yield_time_ms=500)
+        sid = _session_id(initial)
+        result = await stdin_tool.execute(
+            session_id=sid,
+            terminate=True,
+            yield_time_ms=0,
+        )
+        return initial, result
+
+    initial, result = asyncio.run(run())
+    assert "ready" in initial
+    assert "Session terminated." in result
+    assert "Exit code:" in result
+
+
+def test_write_stdin_accepts_max_output_tokens_alias(tmp_path):
+    async def run() -> tuple[str, str, str]:
+        manager = ExecSessionManager()
+        exec_tool = ExecTool(working_dir=str(tmp_path), timeout=5, session_manager=manager)
+        stdin_tool = WriteStdinTool(manager=manager)
+        command = _python_command(
+            "import time; print('A' * 2000, flush=True); time.sleep(5)"
+        )
+
+        initial = await exec_tool.execute(command=command, yield_time_ms=0)
+        sid = _session_id(initial)
+        poll = await stdin_tool.execute(
+            session_id=sid,
+            yield_time_ms=500,
+            max_output_tokens=1000,
+        )
+        cleanup = await stdin_tool.execute(session_id=sid, terminate=True, yield_time_ms=0)
+        return initial, poll, cleanup
+
+    initial, poll, cleanup = asyncio.run(run())
+    assert "Process running" in initial
+    assert "chars truncated" in poll
+    assert "Session terminated." in cleanup
+
+
+def test_write_stdin_preserves_completed_session_output_until_polled(tmp_path):
+    async def run() -> tuple[str, str]:
+        manager = ExecSessionManager()
+        exec_tool = ExecTool(working_dir=str(tmp_path), timeout=5, session_manager=manager)
+        stdin_tool = WriteStdinTool(manager=manager)
+        command = _python_command(
+            "import time; print('ready', flush=True); "
+            "time.sleep(1.0); print('done', flush=True)"
+        )
+
+        initial = await exec_tool.execute(command=command, yield_time_ms=300)
+        sid = _session_id(initial)
+        await asyncio.sleep(1.2)
+        final = await stdin_tool.execute(session_id=sid, chars="", yield_time_ms=0)
+        return initial, final
+
+    initial, final = asyncio.run(run())
+
+    assert "ready" in initial
+    assert "done" in final
+    assert "Exit code: 0" in final
+
+
+def test_write_stdin_can_wait_for_expected_output(tmp_path):
+    async def run() -> tuple[str, str, str]:
+        manager = ExecSessionManager()
+        exec_tool = ExecTool(working_dir=str(tmp_path), timeout=5, session_manager=manager)
+        stdin_tool = WriteStdinTool(manager=manager)
+        command = _python_command(
+            "import time; print('booting', flush=True); "
+            "time.sleep(0.4); print('ready', flush=True); time.sleep(5)"
+        )
+
+        initial = await exec_tool.execute(command=command, yield_time_ms=100)
+        sid = _session_id(initial)
+        waited = await stdin_tool.execute(
+            session_id=sid,
+            wait_for="ready",
+            wait_timeout_ms=3000,
+            yield_time_ms=0,
+        )
+        cleanup = await stdin_tool.execute(session_id=sid, terminate=True, yield_time_ms=0)
+        return initial, waited, cleanup
+
+    initial, waited, cleanup = asyncio.run(run())
+
+    assert "Process running" in initial
+    assert "booting" in initial + waited
+    assert "ready" in waited
+    assert "Wait target not observed" not in waited
+    assert "Session terminated." in cleanup
+
+
+def test_write_stdin_wait_for_reports_timeout_without_killing_session(tmp_path):
+    async def run() -> tuple[str, str, str]:
+        manager = ExecSessionManager()
+        exec_tool = ExecTool(working_dir=str(tmp_path), timeout=5, session_manager=manager)
+        stdin_tool = WriteStdinTool(manager=manager)
+        command = _python_command(
+            "import time; print('booting', flush=True); time.sleep(5)"
+        )
+
+        initial = await exec_tool.execute(command=command, yield_time_ms=100)
+        sid = _session_id(initial)
+        waited = await stdin_tool.execute(
+            session_id=sid,
+            wait_for="never-ready",
+            wait_timeout_ms=200,
+            yield_time_ms=0,
+        )
+        cleanup = await stdin_tool.execute(session_id=sid, terminate=True, yield_time_ms=0)
+        return initial, waited, cleanup
+
+    initial, waited, cleanup = asyncio.run(run())
+
+    assert "Process running" in initial
+    assert "booting" in initial + waited
+    assert "Process running" in waited
+    assert "Wait target not observed: 'never-ready'" in waited
+    assert "Session terminated." in cleanup
+
+
+def test_exec_session_mode_reuses_exec_safety_guard(tmp_path):
+    manager = ExecSessionManager()
+    tool = ExecTool(
+        working_dir=str(tmp_path),
+        deny_patterns=[r"echo\s+blocked"],
+        session_manager=manager,
+    )
+
+    result = asyncio.run(tool.execute(command="echo blocked", yield_time_ms=0))
+
+    assert "blocked by deny pattern" in result
+
+
+def test_write_stdin_reports_missing_session(tmp_path):
+    manager = ExecSessionManager()
+    tool = WriteStdinTool(manager=manager)
+
+    result = asyncio.run(tool.execute(session_id="missing", chars=""))
+
+    assert "exec session not found" in result
+
+
+def test_list_exec_sessions_reports_running_commands(tmp_path):
+    async def run() -> tuple[str, str, str]:
+        manager = ExecSessionManager()
+        exec_tool = ExecTool(working_dir=str(tmp_path), timeout=5, session_manager=manager)
+        list_tool = ListExecSessionsTool(manager=manager)
+        stdin_tool = WriteStdinTool(manager=manager)
+        command = _python_command(
+            "import time; print('ready', flush=True); time.sleep(5)"
+        )
+
+        initial = await exec_tool.execute(command=command, yield_time_ms=500)
+        sid = _session_id(initial)
+        listing = await list_tool.execute()
+        cleanup = await stdin_tool.execute(session_id=sid, terminate=True, yield_time_ms=0)
+        return sid, listing, cleanup
+
+    sid, listing, cleanup = asyncio.run(run())
+
+    assert sid in listing
+    assert "running" in listing
+    assert "elapsed=" in listing
+    assert "remaining=" in listing
+    assert str(tmp_path) in listing
+    assert "Session terminated." in cleanup
+
+
+def test_list_exec_sessions_reports_empty_state():
+    result = asyncio.run(ListExecSessionsTool(manager=ExecSessionManager()).execute())
+
+    assert result == "No active exec sessions."

tests/tools/test_file_edit_coding_enhancements.py

@@ -0,0 +1,216 @@
+from __future__ import annotations
+
+import asyncio
+
+from nanobot.agent.tools.filesystem import EditFileTool, ReadFileTool
+
+
+def test_read_file_force_bypasses_dedup(tmp_path):
+    target = tmp_path / "data.txt"
+    target.write_text("alpha\n")
+    tool = ReadFileTool(workspace=tmp_path)
+
+    first = asyncio.run(tool.execute(path=str(target)))
+    second = asyncio.run(tool.execute(path=str(target)))
+    forced = asyncio.run(tool.execute(path=str(target), force=True))
+
+    assert "alpha" in first
+    assert "unchanged" in second.lower()
+    assert "alpha" in forced
+    assert "unchanged" not in forced.lower()
+
+
+def test_edit_file_can_select_occurrence(tmp_path):
+    target = tmp_path / "duplicate.txt"
+    target.write_text("one\nsame\ntwo\nsame\n")
+    tool = EditFileTool(workspace=tmp_path)
+
+    result = asyncio.run(tool.execute(
+        path=str(target),
+        old_text="same",
+        new_text="changed",
+        occurrence=2,
+    ))
+
+    assert "Successfully edited" in result
+    assert target.read_text() == "one\nsame\ntwo\nchanged\n"
+
+
+def test_edit_file_expected_replacements_guards_replace_all(tmp_path):
+    target = tmp_path / "duplicate.txt"
+    target.write_text("same\nsame\n")
+    tool = EditFileTool(workspace=tmp_path)
+
+    result = asyncio.run(tool.execute(
+        path=str(target),
+        old_text="same",
+        new_text="changed",
+        replace_all=True,
+        expected_replacements=1,
+    ))
+
+    assert "expected 1 replacements but would make 2" in result
+    assert target.read_text() == "same\nsame\n"
+
+
+def test_edit_file_expected_replacements_allows_replace_all_when_count_matches(tmp_path):
+    target = tmp_path / "duplicate.txt"
+    target.write_text("same\nsame\n")
+    tool = EditFileTool(workspace=tmp_path)
+
+    result = asyncio.run(tool.execute(
+        path=str(target),
+        old_text="same",
+        new_text="changed",
+        replace_all=True,
+        expected_replacements=2,
+    ))
+
+    assert "Successfully edited" in result
+    assert target.read_text() == "changed\nchanged\n"
+
+
+def test_edit_file_can_select_nearest_line_hint(tmp_path):
+    target = tmp_path / "duplicate.txt"
+    target.write_text("one\nsame\ntwo\nsame\n")
+    tool = EditFileTool(workspace=tmp_path)
+
+    result = asyncio.run(tool.execute(
+        path=str(target),
+        old_text="same",
+        new_text="changed",
+        line_hint=4,
+    ))
+
+    assert "Successfully edited" in result
+    assert target.read_text() == "one\nsame\ntwo\nchanged\n"
+
+
+def test_edit_file_can_edit_ipynb_as_json(tmp_path):
+    target = tmp_path / "analysis.ipynb"
+    target.write_text('{"cells": []}')
+    tool = EditFileTool(workspace=tmp_path)
+
+    result = asyncio.run(tool.execute(
+        path=str(target),
+        old_text='"cells": []',
+        new_text='"cells": [{"cell_type": "markdown", "source": "hi"}]',
+    ))
+
+    assert "Successfully edited" in result
+    assert '"source": "hi"' in target.read_text()
+
+
+def test_edit_file_multiple_match_hint_mentions_occurrence(tmp_path):
+    target = tmp_path / "duplicate.txt"
+    target.write_text("same\nsame\n")
+    tool = EditFileTool(workspace=tmp_path)
+
+    result = asyncio.run(tool.execute(
+        path=str(target),
+        old_text="same",
+        new_text="changed",
+    ))
+
+    assert "old_text appears 2 times" in result
+    assert "occurrence" in result
+    assert target.read_text() == "same\nsame\n"
+
+
+def test_edit_file_rejects_ambiguous_line_hint(tmp_path):
+    target = tmp_path / "duplicate.txt"
+    target.write_text("same\nmiddle\nsame\n")
+    tool = EditFileTool(workspace=tmp_path)
+
+    result = asyncio.run(tool.execute(
+        path=str(target),
+        old_text="same",
+        new_text="changed",
+        line_hint=2,
+    ))
+
+    assert "line_hint 2 is ambiguous" in result
+    assert target.read_text() == "same\nmiddle\nsame\n"
+
+
+def test_edit_file_rejects_occurrence_with_replace_all(tmp_path):
+    target = tmp_path / "duplicate.txt"
+    target.write_text("same\nsame\n")
+    tool = EditFileTool(workspace=tmp_path)
+
+    result = asyncio.run(tool.execute(
+        path=str(target),
+        old_text="same",
+        new_text="changed",
+        occurrence=1,
+        replace_all=True,
+    ))
+
+    assert "occurrence cannot be used with replace_all" in result
+    assert target.read_text() == "same\nsame\n"
+
+
+def test_edit_file_rejects_line_hint_with_replace_all(tmp_path):
+    target = tmp_path / "duplicate.txt"
+    target.write_text("same\nsame\n")
+    tool = EditFileTool(workspace=tmp_path)
+
+    result = asyncio.run(tool.execute(
+        path=str(target),
+        old_text="same",
+        new_text="changed",
+        line_hint=1,
+        replace_all=True,
+    ))
+
+    assert "line_hint cannot be used with replace_all" in result
+    assert target.read_text() == "same\nsame\n"
+
+
+def test_edit_file_rejects_line_hint_with_occurrence(tmp_path):
+    target = tmp_path / "duplicate.txt"
+    target.write_text("same\nsame\n")
+    tool = EditFileTool(workspace=tmp_path)
+
+    result = asyncio.run(tool.execute(
+        path=str(target),
+        old_text="same",
+        new_text="changed",
+        occurrence=1,
+        line_hint=1,
+    ))
+
+    assert "line_hint cannot be used with occurrence" in result
+    assert target.read_text() == "same\nsame\n"
+
+
+def test_edit_file_rejects_zero_occurrence(tmp_path):
+    target = tmp_path / "duplicate.txt"
+    target.write_text("same\n")
+    tool = EditFileTool(workspace=tmp_path)
+
+    result = asyncio.run(tool.execute(
+        path=str(target),
+        old_text="same",
+        new_text="changed",
+        occurrence=0,
+    ))
+
+    assert "occurrence must be >= 1" in result
+    assert target.read_text() == "same\n"
+
+
+def test_edit_file_rejects_zero_line_hint(tmp_path):
+    target = tmp_path / "duplicate.txt"
+    target.write_text("same\n")
+    tool = EditFileTool(workspace=tmp_path)
+
+    result = asyncio.run(tool.execute(
+        path=str(target),
+        old_text="same",
+        new_text="changed",
+        line_hint=0,
+    ))
+
+    assert "line_hint must be >= 1" in result
+    assert target.read_text() == "same\n"

tests/tools/test_notebook_tool.py

@@ -1,147 +0,0 @@
-"""Tests for NotebookEditTool — Jupyter .ipynb editing."""
-
-import json
-
-import pytest
-
-from nanobot.agent.tools.notebook import NotebookEditTool
-
-
-def _make_notebook(cells: list[dict] | None = None, nbformat: int = 4, nbformat_minor: int = 5) -> dict:
-    """Build a minimal valid .ipynb structure."""
-    return {
-        "nbformat": nbformat,
-        "nbformat_minor": nbformat_minor,
-        "metadata": {"kernelspec": {"display_name": "Python 3", "language": "python", "name": "python3"}},
-        "cells": cells or [],
-    }
-
-
-def _code_cell(source: str, cell_id: str | None = None) -> dict:
-    cell = {"cell_type": "code", "source": source, "metadata": {}, "outputs": [], "execution_count": None}
-    if cell_id:
-        cell["id"] = cell_id
-    return cell
-
-
-def _md_cell(source: str, cell_id: str | None = None) -> dict:
-    cell = {"cell_type": "markdown", "source": source, "metadata": {}}
-    if cell_id:
-        cell["id"] = cell_id
-    return cell
-
-
-def _write_nb(tmp_path, name: str, nb: dict) -> str:
-    p = tmp_path / name
-    p.write_text(json.dumps(nb), encoding="utf-8")
-    return str(p)
-
-
-class TestNotebookEdit:
-
-    @pytest.fixture()
-    def tool(self, tmp_path):
-        return NotebookEditTool(workspace=tmp_path)
-
-    @pytest.mark.asyncio
-    async def test_replace_cell_content(self, tool, tmp_path):
-        nb = _make_notebook([_code_cell("print('hello')"), _code_cell("x = 1")])
-        path = _write_nb(tmp_path, "test.ipynb", nb)
-        result = await tool.execute(path=path, cell_index=0, new_source="print('world')")
-        assert "Successfully" in result
-        saved = json.loads((tmp_path / "test.ipynb").read_text())
-        assert saved["cells"][0]["source"] == "print('world')"
-        assert saved["cells"][1]["source"] == "x = 1"
-
-    @pytest.mark.asyncio
-    async def test_insert_cell_after_target(self, tool, tmp_path):
-        nb = _make_notebook([_code_cell("cell 0"), _code_cell("cell 1")])
-        path = _write_nb(tmp_path, "test.ipynb", nb)
-        result = await tool.execute(path=path, cell_index=0, new_source="inserted", edit_mode="insert")
-        assert "Successfully" in result
-        saved = json.loads((tmp_path / "test.ipynb").read_text())
-        assert len(saved["cells"]) == 3
-        assert saved["cells"][0]["source"] == "cell 0"
-        assert saved["cells"][1]["source"] == "inserted"
-        assert saved["cells"][2]["source"] == "cell 1"
-
-    @pytest.mark.asyncio
-    async def test_delete_cell(self, tool, tmp_path):
-        nb = _make_notebook([_code_cell("A"), _code_cell("B"), _code_cell("C")])
-        path = _write_nb(tmp_path, "test.ipynb", nb)
-        result = await tool.execute(path=path, cell_index=1, edit_mode="delete")
-        assert "Successfully" in result
-        saved = json.loads((tmp_path / "test.ipynb").read_text())
-        assert len(saved["cells"]) == 2
-        assert saved["cells"][0]["source"] == "A"
-        assert saved["cells"][1]["source"] == "C"
-
-    @pytest.mark.asyncio
-    async def test_create_new_notebook_from_scratch(self, tool, tmp_path):
-        path = str(tmp_path / "new.ipynb")
-        result = await tool.execute(path=path, cell_index=0, new_source="# Hello", edit_mode="insert", cell_type="markdown")
-        assert "Successfully" in result or "created" in result.lower()
-        saved = json.loads((tmp_path / "new.ipynb").read_text())
-        assert saved["nbformat"] == 4
-        assert len(saved["cells"]) == 1
-        assert saved["cells"][0]["cell_type"] == "markdown"
-        assert saved["cells"][0]["source"] == "# Hello"
-
-    @pytest.mark.asyncio
-    async def test_invalid_cell_index_error(self, tool, tmp_path):
-        nb = _make_notebook([_code_cell("only cell")])
-        path = _write_nb(tmp_path, "test.ipynb", nb)
-        result = await tool.execute(path=path, cell_index=5, new_source="x")
-        assert "Error" in result
-
-    @pytest.mark.asyncio
-    async def test_non_ipynb_rejected(self, tool, tmp_path):
-        f = tmp_path / "script.py"
-        f.write_text("pass")
-        result = await tool.execute(path=str(f), cell_index=0, new_source="x")
-        assert "Error" in result
-        assert ".ipynb" in result
-
-    @pytest.mark.asyncio
-    async def test_preserves_metadata_and_outputs(self, tool, tmp_path):
-        cell = _code_cell("old")
-        cell["outputs"] = [{"output_type": "stream", "text": "hello\n"}]
-        cell["execution_count"] = 42
-        nb = _make_notebook([cell])
-        path = _write_nb(tmp_path, "test.ipynb", nb)
-        await tool.execute(path=path, cell_index=0, new_source="new")
-        saved = json.loads((tmp_path / "test.ipynb").read_text())
-        assert saved["metadata"]["kernelspec"]["language"] == "python"
-
-    @pytest.mark.asyncio
-    async def test_nbformat_45_generates_cell_id(self, tool, tmp_path):
-        nb = _make_notebook([], nbformat_minor=5)
-        path = _write_nb(tmp_path, "test.ipynb", nb)
-        await tool.execute(path=path, cell_index=0, new_source="x = 1", edit_mode="insert")
-        saved = json.loads((tmp_path / "test.ipynb").read_text())
-        assert "id" in saved["cells"][0]
-        assert len(saved["cells"][0]["id"]) > 0
-
-    @pytest.mark.asyncio
-    async def test_insert_with_cell_type_markdown(self, tool, tmp_path):
-        nb = _make_notebook([_code_cell("code")])
-        path = _write_nb(tmp_path, "test.ipynb", nb)
-        await tool.execute(path=path, cell_index=0, new_source="# Title", edit_mode="insert", cell_type="markdown")
-        saved = json.loads((tmp_path / "test.ipynb").read_text())
-        assert saved["cells"][1]["cell_type"] == "markdown"
-
-    @pytest.mark.asyncio
-    async def test_invalid_edit_mode_rejected(self, tool, tmp_path):
-        nb = _make_notebook([_code_cell("code")])
-        path = _write_nb(tmp_path, "test.ipynb", nb)
-        result = await tool.execute(path=path, cell_index=0, new_source="x", edit_mode="replcae")
-        assert "Error" in result
-        assert "edit_mode" in result
-
-    @pytest.mark.asyncio
-    async def test_invalid_cell_type_rejected(self, tool, tmp_path):
-        nb = _make_notebook([_code_cell("code")])
-        path = _write_nb(tmp_path, "test.ipynb", nb)
-        result = await tool.execute(path=path, cell_index=0, new_source="x", cell_type="raw")
-        assert "Error" in result
-        assert "cell_type" in result

tests/tools/test_search_tools.py

@@ -12,7 +12,7 @@ import pytest
 
 from nanobot.agent.loop import AgentLoop
 from nanobot.agent.subagent import SubagentManager, SubagentStatus
-from nanobot.agent.tools.search import GrepTool
+from nanobot.agent.tools.search import FindFilesTool, GrepTool
 from nanobot.agent.tools.web import WebSearchTool
 from nanobot.bus.queue import MessageBus
 from nanobot.config.schema import WebSearchConfig
@@ -33,6 +33,68 @@ async def test_web_search_tool_refreshes_dynamic_config_loader(monkeypatch) -> N
     assert await tool.execute("nanobot") == "duckduckgo:nanobot:3"
 
 
+@pytest.mark.asyncio
+async def test_find_files_filters_by_query_glob_and_type(tmp_path: Path) -> None:
+    (tmp_path / "src").mkdir()
+    (tmp_path / "src" / "settings_view.tsx").write_text("export {}\n", encoding="utf-8")
+    (tmp_path / "src" / "settings_api.py").write_text("pass\n", encoding="utf-8")
+    (tmp_path / "README.md").write_text("settings\n", encoding="utf-8")
+
+    tool = FindFilesTool(workspace=tmp_path, allowed_dir=tmp_path)
+    result = await tool.execute(
+        path=".",
+        query="settings",
+        glob="src/**",
+        type="ts",
+    )
+
+    assert result.splitlines() == ["src/settings_view.tsx"]
+
+
+@pytest.mark.asyncio
+async def test_find_files_can_include_directories(tmp_path: Path) -> None:
+    (tmp_path / "src" / "settings").mkdir(parents=True)
+    (tmp_path / "src" / "settings" / "index.ts").write_text("export {}\n", encoding="utf-8")
+
+    tool = FindFilesTool(workspace=tmp_path, allowed_dir=tmp_path)
+    result = await tool.execute(path="src", query="settings", include_dirs=True)
+
+    assert "src/settings/" in result.splitlines()
+    assert "src/settings/index.ts" in result.splitlines()
+
+
+@pytest.mark.asyncio
+async def test_find_files_supports_modified_sort_and_pagination(tmp_path: Path) -> None:
+    (tmp_path / "src").mkdir()
+    for idx, name in enumerate(("a.py", "b.py", "c.py"), start=1):
+        file_path = tmp_path / "src" / name
+        file_path.write_text("pass\n", encoding="utf-8")
+        os.utime(file_path, (idx, idx))
+
+    tool = FindFilesTool(workspace=tmp_path, allowed_dir=tmp_path)
+    result = await tool.execute(
+        path="src",
+        type="py",
+        sort="modified",
+        head_limit=1,
+        offset=1,
+    )
+
+    assert result.splitlines()[0] == "src/b.py"
+    assert "pagination: limit=1, offset=1" in result
+
+
+@pytest.mark.asyncio
+async def test_find_files_rejects_paths_outside_workspace(tmp_path: Path) -> None:
+    outside = tmp_path.parent / "outside-find-files.txt"
+    outside.write_text("secret\n", encoding="utf-8")
+
+    tool = FindFilesTool(workspace=tmp_path, allowed_dir=tmp_path)
+    result = await tool.execute(path=str(outside))
+
+    assert result.startswith("Error:")
+
+
 @pytest.mark.asyncio
 async def test_grep_respects_glob_filter_and_context(tmp_path: Path) -> None:
     (tmp_path / "src").mkdir()
@@ -249,6 +311,7 @@ def test_agent_loop_registers_grep(tmp_path: Path) -> None:
 
     loop = AgentLoop(bus=bus, provider=provider, workspace=tmp_path, model="test-model")
 
+    assert "find_files" in loop.tools.tool_names
     assert "grep" in loop.tools.tool_names
 
 
@@ -280,6 +343,7 @@ async def test_subagent_registers_grep(tmp_path: Path) -> None:
     status = SubagentStatus(task_id="sub-1", label="label", task_description="search task", started_at=time.monotonic())
     await mgr._run_subagent("sub-1", "search task", "label", {"channel": "cli", "chat_id": "direct"}, status)
 
+    assert "find_files" in captured["tool_names"]
     assert "grep" in captured["tool_names"]
 
 

tests/tools/test_tool_descriptions.py

@@ -0,0 +1,46 @@
+from nanobot.agent.tools.apply_patch import ApplyPatchTool
+from nanobot.agent.tools.exec_session import ListExecSessionsTool, WriteStdinTool
+from nanobot.agent.tools.filesystem import EditFileTool, ReadFileTool, WriteFileTool
+from nanobot.agent.tools.search import FindFilesTool, GrepTool
+from nanobot.agent.tools.shell import ExecTool
+
+
+def test_coding_tool_descriptions_steer_editing_priority() -> None:
+    apply_patch = ApplyPatchTool().description.lower()
+    edit_file = EditFileTool().description.lower()
+    write_file = WriteFileTool().description.lower()
+
+    assert "default tool for code edits" in apply_patch
+    assert "multi-file" in apply_patch
+    assert "dry_run=true" in apply_patch
+    assert "edit_file only for small exact replacements" in apply_patch
+
+    assert "small, exact replacement" in edit_file
+    assert "copied from read_file" in edit_file
+    assert "prefer apply_patch" in edit_file
+
+    assert "replace an entire file" in write_file
+    assert "prefer apply_patch" in write_file
+
+
+def test_coding_tool_descriptions_steer_discovery_and_shell_usage() -> None:
+    read_file = ReadFileTool().description.lower()
+    find_files = FindFilesTool().description.lower()
+    grep = GrepTool().description.lower()
+    exec_tool = ExecTool().description.lower()
+    write_stdin = WriteStdinTool().description.lower()
+    list_sessions = ListExecSessionsTool().description.lower()
+
+    assert "find_files/list_dir first" in read_file
+    assert "before editing" in read_file
+    assert "prefer it over shell find/ls" in find_files
+    assert "prefer this over shell grep" in grep
+
+    assert "tests, builds" in exec_tool
+    assert "prefer read_file/find_files/grep" in exec_tool
+    assert "apply_patch/write_file/edit_file" in exec_tool
+    assert "yield_time_ms" in exec_tool
+
+    assert "do not use this to start new commands" in write_stdin
+    assert "wait_for" in write_stdin
+    assert "recover a session_id" in list_sessions

tests/tools/test_tool_loader.py

@@ -89,9 +89,11 @@ def test_discover_finds_concrete_tools():
     loader = ToolLoader()
     discovered = loader.discover()
     class_names = {cls.__name__ for cls in discovered}
+    assert "ApplyPatchTool" in class_names
     assert "ExecTool" in class_names
     assert "MessageTool" in class_names
     assert "SpawnTool" in class_names
+    assert "WriteStdinTool" in class_names
 
 
 def test_discover_excludes_abstract_and_mcp():
@@ -406,7 +408,8 @@ def test_loader_registers_same_tools_as_old_hardcoded():
 
     expected = {
         "read_file", "write_file", "edit_file", "list_dir",
-        "grep", "notebook_edit", "exec", "web_search", "web_fetch",
+        "find_files", "grep", "exec", "write_stdin", "list_exec_sessions",
+        "web_search", "web_fetch",
         "message", "spawn", "cron",
     }
     actual = set(registered)

tests/utils/test_file_edit_events.py

@@ -10,6 +10,7 @@ from nanobot.utils.file_edit_events import (
     build_file_edit_start_event,
     line_diff_stats,
     prepare_file_edit_tracker,
+    prepare_file_edit_trackers,
     read_file_snapshot,
 )
 
@@ -81,6 +82,71 @@ def test_binary_file_is_reported_but_not_counted(tmp_path: Path) -> None:
     assert (event["added"], event["deleted"]) == (0, 0)
 
 
+def test_apply_patch_prepares_trackers_for_each_touched_file(tmp_path: Path) -> None:
+    (tmp_path / "src").mkdir()
+    existing = tmp_path / "src" / "existing.py"
+    existing.write_text("old\nkeep\n", encoding="utf-8")
+    delete_me = tmp_path / "src" / "delete_me.py"
+    delete_me.write_text("gone\n", encoding="utf-8")
+
+    patch = """*** Begin Patch
+*** Add File: src/new.py
++fresh
+*** Update File: src/existing.py
+@@
+-old
++new
+ keep
+*** Delete File: src/delete_me.py
+*** End Patch"""
+
+    trackers = prepare_file_edit_trackers(
+        call_id="call-patch",
+        tool_name="apply_patch",
+        tool=None,
+        workspace=tmp_path,
+        params={"patch": patch},
+    )
+
+    assert [tracker.display_path for tracker in trackers] == [
+        "src/new.py",
+        "src/existing.py",
+        "src/delete_me.py",
+    ]
+
+    (tmp_path / "src" / "new.py").write_text("fresh\n", encoding="utf-8")
+    existing.write_text("new\nkeep\n", encoding="utf-8")
+    delete_me.unlink()
+
+    events = [build_file_edit_end_event(tracker, {"patch": patch}) for tracker in trackers]
+    by_path = {event["path"]: event for event in events}
+    assert (by_path["src/new.py"]["added"], by_path["src/new.py"]["deleted"]) == (1, 0)
+    assert (by_path["src/existing.py"]["added"], by_path["src/existing.py"]["deleted"]) == (1, 1)
+    assert (by_path["src/delete_me.py"]["added"], by_path["src/delete_me.py"]["deleted"]) == (0, 1)
+
+
+def test_apply_patch_dry_run_does_not_prepare_file_edit_trackers(tmp_path: Path) -> None:
+    (tmp_path / "file.txt").write_text("old\n", encoding="utf-8")
+
+    trackers = prepare_file_edit_trackers(
+        call_id="call-patch",
+        tool_name="apply_patch",
+        tool=None,
+        workspace=tmp_path,
+        params={
+            "dry_run": True,
+            "patch": """*** Begin Patch
+*** Update File: file.txt
+@@
+-old
++new
+*** End Patch""",
+        },
+    )
+
+    assert trackers == []
+
+
 def test_oversized_write_file_end_uses_known_content_for_exact_count(tmp_path: Path) -> None:
     target = tmp_path / "large.txt"
     params = {"path": "large.txt", "content": "x" * (2 * 1024 * 1024 + 1)}
@@ -140,6 +206,66 @@ def test_streaming_write_file_tracker_emits_live_line_counts(tmp_path: Path) ->
     assert events[-1]["deleted"] == 0
 
 
+def test_streaming_apply_patch_tracker_emits_live_counts_per_file(tmp_path: Path) -> None:
+    (tmp_path / "src").mkdir()
+    (tmp_path / "src" / "existing.py").write_text("old\nkeep\n", encoding="utf-8")
+    events: list[dict] = []
+
+    async def emit(batch: list[dict]) -> None:
+        events.extend(batch)
+
+    async def run() -> None:
+        tracker = StreamingFileEditTracker(workspace=tmp_path, tools={}, emit=emit)
+        await tracker.update({
+            "index": 0,
+            "call_id": "call-patch",
+            "name": "apply_patch",
+            "arguments_delta": (
+                '{"patch":"*** Begin Patch\\n'
+                '*** Update File: src/existing.py\\n'
+                '@@\\n'
+                '-old\\n'
+                '+new\\n'
+                ' keep\\n'
+                '*** Add File: src/new.py\\n'
+                '+fresh\\n'
+            ),
+        })
+
+    asyncio.run(run())
+
+    by_path = {event["path"]: event for event in events}
+    assert by_path["src/existing.py"]["tool"] == "apply_patch"
+    assert by_path["src/existing.py"]["status"] == "editing"
+    assert by_path["src/existing.py"]["approximate"] is True
+    assert (by_path["src/existing.py"]["added"], by_path["src/existing.py"]["deleted"]) == (1, 1)
+    assert (by_path["src/new.py"]["added"], by_path["src/new.py"]["deleted"]) == (1, 0)
+
+
+def test_streaming_apply_patch_tracker_skips_dry_run(tmp_path: Path) -> None:
+    events: list[dict] = []
+
+    async def emit(batch: list[dict]) -> None:
+        events.extend(batch)
+
+    async def run() -> None:
+        tracker = StreamingFileEditTracker(workspace=tmp_path, tools={}, emit=emit)
+        await tracker.update({
+            "index": 0,
+            "call_id": "call-patch",
+            "name": "apply_patch",
+            "arguments_delta": (
+                '{"dry_run":true,"patch":"*** Begin Patch\\n'
+                '*** Add File: dry.md\\n'
+                '+preview\\n'
+            ),
+        })
+
+    asyncio.run(run())
+
+    assert events == []
+
+
 def test_streaming_write_file_tracker_emits_pending_before_path(tmp_path: Path) -> None:
     events: list[dict] = []