Add file manipulation tools and enhance setup scripts

- Introduced file manipulation capabilities in `model_tools.py`, including functions for reading, writing, patching, and searching files.
- Added a new `file` toolset in `toolsets.py` and updated distributions to include file tools.
- Enhanced `setup-hermes.sh` and `install.sh` scripts to check for and optionally install `ripgrep` for faster file searching.
- Implemented a new `file_operations.py` module to encapsulate file operations using shell commands.
- Updated `doctor.py` and `install.ps1` to check for `ripgrep` and provide installation guidance if not found.
- Added fuzzy matching and patch parsing capabilities to improve file manipulation accuracy and flexibility.

tools/file_tools.py

@@ -0,0 +1,113 @@
+#!/usr/bin/env python3
+"""File Tools Module - LLM agent file manipulation tools."""
+
+import json
+import threading
+from typing import Optional
+from tools.file_operations import ShellFileOperations
+
+_file_ops_lock = threading.Lock()
+_file_ops_cache: dict = {}
+
+
+def _get_file_ops(task_id: str = "default") -> ShellFileOperations:
+    """Get or create ShellFileOperations for a terminal environment."""
+    from tools.terminal_tool import _active_environments, _env_lock, _LocalEnvironment
+    
+    with _file_ops_lock:
+        if task_id in _file_ops_cache:
+            return _file_ops_cache[task_id]
+        
+        with _env_lock:
+            if task_id not in _active_environments:
+                import os
+                env = _LocalEnvironment(cwd=os.getcwd(), timeout=60)
+                _active_environments[task_id] = env
+            terminal_env = _active_environments[task_id]
+        
+        file_ops = ShellFileOperations(terminal_env)
+        _file_ops_cache[task_id] = file_ops
+        return file_ops
+
+
+def clear_file_ops_cache(task_id: str = None):
+    """Clear the file operations cache."""
+    with _file_ops_lock:
+        if task_id:
+            _file_ops_cache.pop(task_id, None)
+        else:
+            _file_ops_cache.clear()
+
+
+def read_file_tool(path: str, offset: int = 1, limit: int = 500, task_id: str = "default") -> str:
+    """Read a file with pagination and line numbers."""
+    try:
+        file_ops = _get_file_ops(task_id)
+        result = file_ops.read_file(path, offset, limit)
+        return json.dumps(result.to_dict(), ensure_ascii=False)
+    except Exception as e:
+        return json.dumps({"error": str(e)}, ensure_ascii=False)
+
+
+def write_file_tool(path: str, content: str, task_id: str = "default") -> str:
+    """Write content to a file."""
+    try:
+        file_ops = _get_file_ops(task_id)
+        result = file_ops.write_file(path, content)
+        return json.dumps(result.to_dict(), ensure_ascii=False)
+    except Exception as e:
+        return json.dumps({"error": str(e)}, ensure_ascii=False)
+
+
+def patch_tool(mode: str = "replace", path: str = None, old_string: str = None,
+               new_string: str = None, replace_all: bool = False, patch: str = None,
+               task_id: str = "default") -> str:
+    """Patch a file using replace mode or V4A patch format."""
+    try:
+        file_ops = _get_file_ops(task_id)
+        
+        if mode == "replace":
+            if not path:
+                return json.dumps({"error": "path required"})
+            if old_string is None or new_string is None:
+                return json.dumps({"error": "old_string and new_string required"})
+            result = file_ops.patch_replace(path, old_string, new_string, replace_all)
+        elif mode == "patch":
+            if not patch:
+                return json.dumps({"error": "patch content required"})
+            result = file_ops.patch_v4a(patch)
+        else:
+            return json.dumps({"error": f"Unknown mode: {mode}"})
+        
+        return json.dumps(result.to_dict(), ensure_ascii=False)
+    except Exception as e:
+        return json.dumps({"error": str(e)}, ensure_ascii=False)
+
+
+def search_tool(pattern: str, target: str = "content", path: str = ".",
+                file_glob: str = None, limit: int = 50, offset: int = 0,
+                output_mode: str = "content", context: int = 0,
+                task_id: str = "default") -> str:
+    """Search for content or files."""
+    try:
+        file_ops = _get_file_ops(task_id)
+        result = file_ops.search(
+            pattern=pattern, path=path, target=target, file_glob=file_glob,
+            limit=limit, offset=offset, output_mode=output_mode, context=context
+        )
+        return json.dumps(result.to_dict(), ensure_ascii=False)
+    except Exception as e:
+        return json.dumps({"error": str(e)}, ensure_ascii=False)
+
+
+FILE_TOOLS = [
+    {"name": "read_file", "function": read_file_tool},
+    {"name": "write_file", "function": write_file_tool},
+    {"name": "patch", "function": patch_tool},
+    {"name": "search", "function": search_tool}
+]
+
+
+def get_file_tools():
+    """Get the list of file tool definitions."""
+    return FILE_TOOLS