feat(tools): optimize coding workflows

tests/tools/test_apply_patch_tool.py

@@ -0,0 +1,238 @@
+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 target.read_text() == "line1\nchanged2\nline3\nchanged4\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:
-    """edit_file should refuse .ipynb and suggest notebook_edit."""
+class TestEditIpynbFiles:
+    """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")
-        assert "notebook" in result.lower()
+        result = await tool.execute(
+            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_session_tools.py

@@ -0,0 +1,242 @@
+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, 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 "got:ping" in result
+    assert "Exit code: 0" 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_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

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_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 +408,7 @@ 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",
+        "grep", "exec", "web_search", "web_fetch",
         "message", "spawn", "cron",
     }
     actual = set(registered)