Add Phase 6: write tools, shell, and edit tools with reasoning-only fix

Implement 6 new agent tools — write_file, make_dir, delete_file,
str_replace, patch_apply, run_command — bringing the agent from
read-only observer to active code modifier. All write/shell operations
are gated through the existing permissions service.

Also fix a bug where qwen3.5 thinking mode produces reasoning tokens
but no content after tool results, causing the agent to silently exit.
The loop now detects reasoning-only responses, retries twice, then
injects a nudge message to break the model out of its thinking loop.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

app/tools/registry.py

@@ -38,14 +38,47 @@ class ToolRegistry:
 
 def create_default_registry(workspace_root: Path, config: AppConfig) -> ToolRegistry:
     """Create a ToolRegistry populated with all built-in tools."""
+    # Read tools
     from app.tools.filesystem import ListDirTool, ReadFileTool
+
+    # Write tools
+    from app.tools.filesystem import DeleteFileTool, MakeDirTool, WriteFileTool
+
+    # Edit tools
+    from app.tools.edit import PatchApplyTool, StrReplaceTool
+
+    # Shell tools
+    from app.tools.shell import RunCommandTool
+
+    # Control flow
     from app.tools.finish import FinishTool
+
+    # Search tools
     from app.tools.search import FindFilesTool, GrepFilesTool
 
     registry = ToolRegistry()
+
+    # Read
     registry.register(ReadFileTool(workspace_root, config))
     registry.register(ListDirTool(workspace_root, config))
+
+    # Search
     registry.register(GrepFilesTool(workspace_root, config))
     registry.register(FindFilesTool(workspace_root, config))
+
+    # Write
+    registry.register(WriteFileTool(workspace_root, config))
+    registry.register(MakeDirTool(workspace_root, config))
+    registry.register(DeleteFileTool(workspace_root, config))
+
+    # Edit
+    registry.register(StrReplaceTool(workspace_root, config))
+    registry.register(PatchApplyTool(workspace_root, config))
+
+    # Shell
+    registry.register(RunCommandTool(workspace_root, config))
+
+    # Control flow
     registry.register(FinishTool(workspace_root, config))
+
     return registry