improve file editing and add notebook tool

Enhance file tools with read tracking, PDF support, safer path handling,
smarter edit matching/diagnostics, and introduce notebook_edit with tests.

tests/tools/test_edit_enhancements.py

@@ -0,0 +1,152 @@
+"""Tests for EditFileTool enhancements: read-before-edit tracking, path suggestions,
+.ipynb detection, and create-file semantics."""
+
+import pytest
+
+from nanobot.agent.tools.filesystem import EditFileTool, ReadFileTool, WriteFileTool
+from nanobot.agent.tools import file_state
+
+
+# ---------------------------------------------------------------------------
+# Helpers
+# ---------------------------------------------------------------------------
+
+@pytest.fixture(autouse=True)
+def _clear_file_state():
+    """Reset global read-state between tests."""
+    file_state.clear()
+    yield
+    file_state.clear()
+
+
+# ---------------------------------------------------------------------------
+# Read-before-edit tracking
+# ---------------------------------------------------------------------------
+
+class TestEditReadTracking:
+    """edit_file should warn when file hasn't been read first."""
+
+    @pytest.fixture()
+    def read_tool(self, tmp_path):
+        return ReadFileTool(workspace=tmp_path)
+
+    @pytest.fixture()
+    def edit_tool(self, tmp_path):
+        return EditFileTool(workspace=tmp_path)
+
+    @pytest.mark.asyncio
+    async def test_edit_warns_if_file_not_read_first(self, edit_tool, tmp_path):
+        f = tmp_path / "a.py"
+        f.write_text("hello world", encoding="utf-8")
+        result = await edit_tool.execute(path=str(f), old_text="world", new_text="earth")
+        # Should still succeed but include a warning
+        assert "Successfully" in result
+        assert "not been read" in result.lower() or "warning" in result.lower()
+
+    @pytest.mark.asyncio
+    async def test_edit_succeeds_cleanly_after_read(self, read_tool, edit_tool, tmp_path):
+        f = tmp_path / "a.py"
+        f.write_text("hello world", encoding="utf-8")
+        await read_tool.execute(path=str(f))
+        result = await edit_tool.execute(path=str(f), old_text="world", new_text="earth")
+        assert "Successfully" in result
+        # No warning when file was read first
+        assert "not been read" not in result.lower()
+        assert f.read_text() == "hello earth"
+
+    @pytest.mark.asyncio
+    async def test_edit_warns_if_file_modified_since_read(self, read_tool, edit_tool, tmp_path):
+        f = tmp_path / "a.py"
+        f.write_text("hello world", encoding="utf-8")
+        await read_tool.execute(path=str(f))
+        # External modification
+        f.write_text("hello universe", encoding="utf-8")
+        result = await edit_tool.execute(path=str(f), old_text="universe", new_text="earth")
+        assert "Successfully" in result
+        assert "modified" in result.lower() or "warning" in result.lower()
+
+
+# ---------------------------------------------------------------------------
+# Create-file semantics
+# ---------------------------------------------------------------------------
+
+class TestEditCreateFile:
+    """edit_file with old_text='' creates new file if not exists."""
+
+    @pytest.fixture()
+    def tool(self, tmp_path):
+        return EditFileTool(workspace=tmp_path)
+
+    @pytest.mark.asyncio
+    async def test_create_new_file_with_empty_old_text(self, tool, tmp_path):
+        f = tmp_path / "subdir" / "new.py"
+        result = await tool.execute(path=str(f), old_text="", new_text="print('hi')")
+        assert "created" in result.lower() or "Successfully" in result
+        assert f.exists()
+        assert f.read_text() == "print('hi')"
+
+    @pytest.mark.asyncio
+    async def test_create_fails_if_file_already_exists_and_not_empty(self, tool, tmp_path):
+        f = tmp_path / "existing.py"
+        f.write_text("existing content", encoding="utf-8")
+        result = await tool.execute(path=str(f), old_text="", new_text="new content")
+        assert "Error" in result or "already exists" in result.lower()
+        # File should be unchanged
+        assert f.read_text() == "existing content"
+
+    @pytest.mark.asyncio
+    async def test_create_succeeds_if_file_exists_but_empty(self, tool, tmp_path):
+        f = tmp_path / "empty.py"
+        f.write_text("", encoding="utf-8")
+        result = await tool.execute(path=str(f), old_text="", new_text="print('hi')")
+        assert "Successfully" in result
+        assert f.read_text() == "print('hi')"
+
+
+# ---------------------------------------------------------------------------
+# .ipynb detection
+# ---------------------------------------------------------------------------
+
+class TestEditIpynbDetection:
+    """edit_file should refuse .ipynb and suggest notebook_edit."""
+
+    @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):
+        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()
+
+
+# ---------------------------------------------------------------------------
+# Path suggestion on not-found
+# ---------------------------------------------------------------------------
+
+class TestEditPathSuggestion:
+    """edit_file should suggest similar paths on not-found."""
+
+    @pytest.fixture()
+    def tool(self, tmp_path):
+        return EditFileTool(workspace=tmp_path)
+
+    @pytest.mark.asyncio
+    async def test_suggests_similar_filename(self, tool, tmp_path):
+        f = tmp_path / "config.py"
+        f.write_text("x = 1", encoding="utf-8")
+        # Typo: conifg.py
+        result = await tool.execute(
+            path=str(tmp_path / "conifg.py"), old_text="x = 1", new_text="x = 2",
+        )
+        assert "Error" in result
+        assert "config.py" in result
+
+    @pytest.mark.asyncio
+    async def test_shows_cwd_in_error(self, tool, tmp_path):
+        result = await tool.execute(
+            path=str(tmp_path / "nonexistent.py"), old_text="a", new_text="b",
+        )
+        assert "Error" in result