feat:[response API] GPT 5.1 apply_patch tool call support

[priyansh4320]

Why are these changes needed?

This pull request is a short PR adding apply patch tool call support for gpt-5.1 and codex models

• added type safety for built in tools params
• updated client and message retrieval for apply_tool support

Related issue number

#2211

Checks

• [x] I've included any doc changes needed for https://docs.ag2.ai/. See https://docs.ag2.ai/latest/docs/contributor-guide/documentation/ to build and test documentation locally.
• [x] I've added tests (if relevant) corresponding to the changes introduced in this PR.
• [x] I've made sure all auto checks have passed.

[joggrbot[bot]]

📝 Documentation Analysis

All docs are up to date! 🎉

---

✅ Latest commit analyzed: 3463db8caa0763524da85dbc9665abb7ceea02c7 | Powered by Joggr

[elCaptnCode]

I am really looking forward to this integration.

[randombet]

@claude How apply patch is supported in AG2 here? Reference https://platform.openai.com/docs/guides/tools-apply-patch

[claude[bot]]

Claude finished @randombet's task —— View job

---

How apply_patch is supported in AG2

I've analyzed the PR implementation and can explain how apply_patch support works in AG2, following OpenAI's Responses API design pattern.

---

Architecture Overview

The apply_patch tool in AG2 follows OpenAI's Responses API pattern with three main components:

1. Core Tool Implementation (autogen/tools/apply_patch_tool.py)

This provides the file operations engine with two main classes:

WorkspaceEditor: Filesystem abstraction that:

• Manages file operations within a workspace directory
• Enforces security through allowed_paths patterns (supports glob patterns like **, src/**)
• Applies unified diffs using the custom _V4ADiffApplier
• Supports three operations: create_file, update_file, delete_file
• Works with both sync and async operations

ApplyPatchTool: AG2 Tool wrapper that:

• Integrates WorkspaceEditor with the AG2 agent framework
• Handles approval workflows via needs_approval and on_approval callbacks
• Provides both sync and async patch application

2. Responses API Client Integration (autogen/oai/openai_responses.py)

The OpenAIResponsesClient handles the conversation flow:

Key Method: _apply_patch_operation() (lines 229-330)

• Creates a WorkspaceEditor instance with workspace_dir and allowed_paths
• Routes operations to appropriate handlers (create/update/delete)
• Handles async execution (with event loop detection for Jupyter compatibility)
• Returns ApplyPatchCallOutput dataclass with status and output

Message Processing: _normalize_messages_for_responses_api() (lines 332-490)

• Extracts apply_patch_call items from messages
• Executes patch operations and converts them to apply_patch_call_output
• Handles both current message patches and continuation from previous responses
• Filters out already-processed patch calls to avoid duplication

Request Building (lines 495-550):

• Adds {"type": "apply_patch"} to the tools list when apply_patch or apply_patch_async is in built_in_tools
• Retrieves previous response to check for pending apply_patch_calls

3. Configuration Integration (autogen/oai/client.py)

Extends OpenAILLMConfigEntry with new fields (lines 259-260, 282-283):

workspace_dir: str | None
allowed_paths: list[str] | None

And adds to create() method signature (lines 1625-1629):

built_in_tools: list[Literal["web_search", "image_generation", "apply_patch", "apply_patch_async"]]
workspace_dir: str | None = None
allowed_paths: list[str] | None = None

---

Usage Pattern

Based on the example notebook (notebook/agentchat_gpt5.1_apply_patch_example.ipynb), here's how to use it:

Simple Usage (Automatic Setup)

llm_config = LLMConfig(
    config_list={
        "api_type": "responses",
        "model": "gpt-5.1",
        "api_key": os.getenv("OPENAI_API_KEY"),
        "built_in_tools": ["apply_patch"],  # or "apply_patch_async"
        "workspace_dir": "./my_project_folder",  # Optional, defaults to cwd
        "allowed_paths": ["src/**", "tests/**"],  # Optional, defaults to ["**"]
    },
)

coding_agent = ConversableAgent(
    name="coding_assistant",
    llm_config=llm_config,
    system_message="You are a helpful coding assistant...",
)

# Agent automatically has access to apply_patch tool
result = coding_agent.initiate_chat(
    recipient=coding_agent,
    message="Create src/main.py with a hello world function",
    max_turns=2,
)

Advanced Usage (Manual Tool Registration)

from autogen.tools import ApplyPatchTool, WorkspaceEditor

editor = WorkspaceEditor(
    workspace_dir="./my_project",
    allowed_paths=["src/**", "*.py"]
)

patch_tool = ApplyPatchTool(
    editor=editor,
    needs_approval=True,
    on_approval=lambda ctx, item: {"approve": True}
)

agent = ConversableAgent(
    name="coding_assistant",
    llm_config={"api_type": "responses", "model": "gpt-5.1", ...}
)
patch_tool.register_tool(agent)

---

Key Features

1. Security: Path validation ensures operations stay within workspace and match allowed patterns
2. Flexibility: Supports both sync (apply_patch) and async (apply_patch_async) modes
3. Approval Workflow: Optional needs_approval parameter for user confirmation
4. Unified Diff Format: Uses standard diff format for precise file modifications
5. Error Handling: Comprehensive error messages for failed operations
6. Multi-Agent Support: Works in groupchat scenarios with multiple agents (see notebook examples)

---

Diff Format

The tool uses unified diff format. Example from the implementation:

@@ -1,3 +1,3 @@
 def hello():
-    print("World")
+    print("Hello, World!")
     return True

GPT-5.1 generates these diffs automatically when using the apply_patch tool.

---

Integration Points

The integration touches several key areas:

1. Type Safety (autogen/oai/openai_responses.py:55-63): New ApplyPatchCallOutput dataclass
2. Client Extensions (autogen/oai/client.py): New config fields for workspace_dir and allowed_paths
3. Message Normalization (autogen/oai/openai_responses.py:332-490): Processes apply_patch_call items in conversation flow
4. Code Utils (autogen/code_utils.py): Enhanced to handle apply_patch operations
5. Tests: Comprehensive test coverage in test/tools/test_apply_patch_tool.py and test/oai/test_responses_client.py

---

Answering the Original Question

The ApplyPatchTool is used automatically when you:

1. Set api_type: "responses" with model: "gpt-5.1"
2. Include "apply_patch" or "apply_patch_async" in built_in_tools
3. Optionally configure workspace_dir and allowed_paths

The tool doesn't need explicit registration in the simple case - the OpenAIResponsesClient automatically handles apply_patch_call items in the conversation and executes them via _apply_patch_operation().

The notebook (notebook/agentchat_gpt5.1_apply_patch_example.ipynb) demonstrates various usage scenarios including single-agent, two-agent, and groupchat examples with file creation, modification, and deletion operations.

---

[randombet]

@priyansh4320 Awesome feature! I will try review it asap.

[randombet]

@claude Review this PR.

[claude[bot]]

Claude finished @randombet's task —— View job

---

Code Review Complete ✅

I've completed a thorough review of PR #2213. This is a substantial feature addition that implements GPT-5.1's apply_patch tool support in AG2. Overall, the implementation is well-architected with good test coverage, but there are several issues that should be addressed before merging.

---

Summary

This PR adds support for OpenAI's Responses API apply_patch tool, enabling GPT-5.1 and codex models to create, update, and delete files using unified diffs. The implementation includes:

• New tool: ApplyPatchTool with WorkspaceEditor for file operations (512 lines)
• Client integration: Extended OpenAIResponsesClient to handle apply_patch calls (334 additions)
• Configuration: Added workspace_dir and allowed_paths to LLM config
• Tests: Comprehensive test suite (520 + 1148 lines)
• Example: Jupyter notebook demonstrating usage (42 cells)

---

Critical Issues 🔴

1. Debug Print Statement Left in Production Code

Location: autogen/oai/openai_responses.py:622

print("params", params)

Impact: This debug statement will spam logs in production.

Fix: Remove this line immediately.

---

2. Async Implementation Issues

Location: autogen/tools/apply_patch_tool.py:284-303

The async methods (a_create_file, a_update_file, a_delete_file) are identical to their sync counterparts - they don't actually perform any async I/O operations. They just call synchronous Path.write_text() and Path.read_text().

async def a_create_file(self, operation: dict[str, Any]) -> dict[str, Any]:
    """Create a new file."""
    try:
        # ... same code as create_file ...
        full_path.write_text(content, encoding="utf-8")  # ⚠️ Still blocking!

Impact:

• Misleading API - users expect true async behavior
• Event loop blocking - defeats the purpose of async
• The complex thread-based workaround in openai_responses.py:258-271 wouldn't be needed if these were truly async

Fix: Either:

1. Use aiofiles for true async file I/O, or
2. Remove the async variants and document that file operations are synchronous

---

3. Path Validation Logic Has Edge Cases

Location: autogen/tools/apply_patch_tool.py:214-261

The _validate_path method has problematic logic:

# Check if path matches any allowed pattern first (works for both local and cloud paths)
matches_any = False
for pattern in self.allowed_paths:
    # ...
    if fnmatch.fnmatch(path_normalized, pattern_normalized):
        matches_any = True
        break

if not matches_any:
    raise ValueError(f"Path {path} is not allowed...")

# For local filesystem paths, validate they're within workspace
try:
    full_path = (Path(self.workspace_dir) / path).resolve()
    
    if not str(full_path).startswith(str(self.workspace_dir)):
        raise ValueError(f"Path {path} is outside workspace directory")
    
    return full_path
except (OSError, ValueError) as e:
    # If path resolution fails, it might be a cloud storage path
    if matches_any:
        return Path(path)  # ⚠️ This won't work for actual file ops
    raise ValueError(f"Path {path} is invalid: {str(e)}")

Issues:

1. Cloud storage support is incomplete - The code claims to support cloud storage paths (S3, etc.) but returns a local Path object that can't actually access cloud storage
2. Pattern matching uses fnmatch instead of pathlib.Path.match - fnmatch doesn't properly handle ** for recursive matching (it treats it literally)
3. String prefix checking is unsafe - Using str().startswith() for path validation is vulnerable to path traversal (e.g., /workspace vs /workspace_evil)

Fix:

# Use pathlib for proper ** matching
from pathlib import PurePath

def _validate_path(self, path: str) -> Path:
    # Check allowed patterns using pathlib (proper ** support)
    matches_any = any(
        PurePath(path).match(pattern) 
        for pattern in self.allowed_paths
    )
    
    if not matches_any:
        raise ValueError(f"Path {path} not allowed by patterns")
    
    # Validate within workspace
    full_path = (self.workspace_dir / path).resolve()
    
    # Use is_relative_to (Python 3.9+) or proper path comparison
    try:
        full_path.relative_to(self.workspace_dir)
    except ValueError:
        raise ValueError(f"Path {path} is outside workspace")
    
    return full_path

And remove cloud storage claims from documentation unless you actually implement cloud storage support.

---

Major Issues 🟠

4. Type Safety Violations

Location: Multiple places with # type: ignore[arg-type]

full_path = self._validate_path(path)  # type: ignore[arg-type]

Issue: The type checkers are warning that path might be None (from operation.get("path")), but you're suppressing instead of handling.

Fix:

path = operation.get("path")
if not path:
    return {"status": "failed", "output": "Missing 'path' in operation"}

diff = operation.get("diff", "")
full_path = self._validate_path(path)

---

5. Error Messages Expose Internal Paths

Location: All file operation methods

return {"status": "failed", "output": f"Error creating {path}: {str(e)}"}

Security Issue: Stack traces in str(e) might expose sensitive filesystem information to the LLM/user.

Fix: Sanitize error messages or use structured error types.

---

6. Diff Applier Edge Cases

Location: autogen/tools/apply_patch_tool.py:86-173

The _V4ADiffApplier is well-implemented overall, but has some edge cases:

def _consume_hunk_line(self, line: str) -> None:
    if not line or line.startswith("\\ No newline"):
        return
    prefix = line[0] if line else " "  # ⚠️ line[0] after checking "if not line"?
    payload = line[1:] if len(line) > 1 and prefix in "+- " else line

Issue: The logic checks if not line but then accesses line[0] in the same expression. The ternary makes prefix = " " when line is empty, but it's confusing.

Minor: Not a bug, just harder to read than necessary.

---

7. Missing Input Validation

Location: autogen/oai/openai_responses.py:_apply_patch_operation

The operation dict from the LLM is not validated before use:

operation = apply_patch_call.get("operation", {})
if operation:
    output = self._apply_patch_operation(operation, ...)

Issue: No validation that operation["type"] is a valid operation, or that required fields exist.

Fix: Add validation:

VALID_OPERATIONS = {"create_file", "update_file", "delete_file"}

op_type = operation.get("type")
if op_type not in VALID_OPERATIONS:
    return ApplyPatchCallOutput(
        call_id=call_id,
        status="failed", 
        output=f"Invalid operation type: {op_type}"
    )

---

Code Quality Issues 🟡

8. Inconsistent Return Types

Location: autogen/tools/apply_patch_tool.py:ApplyPatchTool.__init__

The handler function returns different shapes:

# Sometimes returns this format:
{"type": "apply_patch_call_output", "call_id": call_id, **result}

# But result itself is:
{"status": "completed", "output": "..."}

# So the final shape is:
{"type": "apply_patch_call_output", "call_id": call_id, "status": "completed", "output": "..."}

But in openai_responses.py, you also have an ApplyPatchCallOutput dataclass. The two representations should be unified.

---

9. Code Duplication

Locations:

• autogen/oai/openai_responses.py:379-403 vs 405-428
• Sync vs async file operations

Both blocks of code for processing message_apply_patch_calls vs previous_apply_patch_calls are nearly identical. This should be refactored:

def _process_patch_calls(self, patch_calls_dict, workspace_dir, allowed_paths, async_mode):
    """Process apply_patch_call items and return outputs."""
    outputs = []
    for call_id, apply_patch_call in patch_calls_dict.items():
        operation = apply_patch_call.get("operation", {})
        if operation:
            output = self._apply_patch_operation(
                operation, call_id, workspace_dir, 
                allowed_paths, async_patches=async_mode
            )
            outputs.append(output.to_dict())
    return outputs

# Then use it:
message_outputs = self._process_patch_calls(
    message_apply_patch_calls, workspace_dir, allowed_paths,
    async_mode="apply_patch_async" in built_in_tools
)

---

10. Thread Safety Concerns

Location: autogen/oai/openai_responses.py:258-271

The _run_async_in_thread helper creates a new thread with a new event loop for every async operation:

def _run_async_in_thread(coro):
    result = {}
    def runner():
        loop = asyncio.new_event_loop()
        asyncio.set_event_loop(loop)
        result["value"] = loop.run_until_complete(coro)
        loop.close()
    
    t = threading.Thread(target=runner)
    t.start()
    t.join()
    return result["value"]

Issues:

1. Creates a new thread for every file operation - expensive
2. No timeout - could hang forever
3. Using mutable dict for return value is a code smell

Fix: Since the file operations aren't truly async anyway (see issue #2), just make them synchronous.

---

11. Message Processing Logic is Complex

Location: autogen/oai/openai_responses.py:332-491

The _normalize_messages_for_responses_api method is 160 lines and handles multiple concerns:

• Extracting apply_patch_calls from messages
• Processing those calls
• Retrieving previous response calls
• Converting messages to Responses API format
• Handling image params
• Filtering processed calls

Recommendation: Break this into smaller, focused methods:

• _extract_apply_patch_calls(messages) -> dict
• _execute_apply_patch_calls(calls_dict, ...) -> list
• _convert_messages_to_input(messages, ...) -> list

---

Minor Issues / Suggestions 💡

12. Documentation Improvements

Location: autogen/tools/apply_patch_tool.py:184-207

The docstring claims cloud storage support but it's not actually implemented:

"""File system editor for apply_patch operations.

Supports both local filesystem and cloud storage paths through allowed_paths patterns.

Fix: Remove cloud storage claims or implement it properly.

---

13. Test Coverage Gaps

While test coverage is good overall (77.2%), there are some gaps:

Missing coverage in autogen/code_utils.py: The new apply_patch_call handling in content_str() has 0% coverage (lines 86-93).

Test file: test/test_llm_config.py - 101 new lines but need to verify they test the new workspace_dir and allowed_paths fields.

---

14. Naming Inconsistency

You have both:

• apply_patch (synchronous)
• apply_patch_async (asynchronous)

But the underlying tool methods are:

• create_file / a_create_file
• update_file / a_update_file
• delete_file / a_delete_file

Consider making the naming consistent - either _async suffix or a_ prefix throughout.

---

15. Hardcoded Defaults

Location: autogen/tools/apply_patch_tool.py:212

self.allowed_paths = allowed_paths or ["**"]

Defaulting to ["**"] (allow all files) is insecure by default. Consider:

self.allowed_paths = allowed_paths or []  # Deny all by default
# Or at minimum, document the security implications clearly

---

16. Protocol Definition Could Be Simpler

Location: autogen/tools/apply_patch_tool.py:16-83

The PatchEditor Protocol defines both sync and async methods, but most implementations will only support one or the other. Consider:

class SyncPatchEditor(Protocol):
    def create_file(...) -> dict: ...
    def update_file(...) -> dict: ...
    def delete_file(...) -> dict: ...

class AsyncPatchEditor(Protocol):
    async def create_file(...) -> dict: ...
    async def update_file(...) -> dict: ...
    async def delete_file(...) -> dict: ...

Then let WorkspaceEditor implement both if needed.

---

Positive Aspects ✅

1. Excellent test coverage - 520 lines of tool tests + 1148 lines of client tests
2. Good separation of concerns - Tool layer separate from client integration
3. Security-conscious - Path validation, allowed_paths patterns
4. Good error handling - Operations return structured status/output dicts
5. Well-documented - Docstrings with examples
6. Comprehensive notebook example - Shows real usage patterns
7. Type hints - Good use of type annotations throughout
8. Backwards compatible - New features don't break existing code

---

Recommendations

Must Fix Before Merge:

1. ❌ Remove debug print() statement (line 622)
2. ❌ Fix path validation security issues (use Path.relative_to() instead of string prefix)
3. ❌ Fix or remove incomplete cloud storage support
4. ❌ Add input validation for operation types

Should Fix Before Merge:

5. ⚠️ Make async truly async or remove async variants
6. ⚠️ Fix type ignore comments with proper null checks
7. ⚠️ Refactor duplicated code in message processing
8. ⚠️ Add test coverage for content_str() apply_patch_call handling

Nice to Have:

9. 💡 Improve error message sanitization
10. 💡 Reconsider default allowed_paths = ["**"] security
11. 💡 Refactor long _normalize_messages_for_responses_api method
12. 💡 Consider thread pool instead of one-thread-per-operation

---

Test Coverage Note

Codecov shows 77.2% patch coverage with 88 lines missing. The main gaps are:

• autogen/oai/openai_responses.py: 32 missing + 13 partials (mostly async execution paths)
• autogen/tools/apply_patch_tool.py: 28 missing + 8 partials (error paths)
• autogen/code_utils.py: 6 missing + 1 partial (new apply_patch_call handling)

This is reasonable for a first implementation, but aim to increase coverage above 85% for critical security code like path validation.

---

Conclusion

This is a well-architected feature that adds valuable GPT-5.1 capabilities to AG2. The core design is solid, tests are comprehensive, and documentation is good. However, there are several critical issues (debug print, path security, async implementation) that must be addressed before merging.

The code quality is generally high, but would benefit from:

• Removing the debug print statement
• Fixing path validation security
• Clarifying async behavior (make it truly async or remove it)
• Adding input validation
• Reducing code duplication

Once these issues are addressed, this will be a great addition to AG2! 🚀

---

Files reviewed:

• autogen/tools/apply_patch_tool.py (512 lines) ✓
• autogen/oai/openai_responses.py (+334 lines) ✓
• autogen/oai/client.py (+9 lines) ✓
• autogen/code_utils.py (+8 lines) ✓
• test/tools/test_apply_patch_tool.py (520 lines) ✓
• test/oai/test_responses_client.py (+1148 lines) ✓
• notebook/agentchat_gpt5.1_apply_patch_example.ipynb (42 cells) ✓

---

[randombet]

@priyansh4320 I think the PR is good. A few minor changes needs to be completed and a few follow-ups to be done. I want to highlight this feature in the next release.

Changes need to be done:

1. Move ApplyPatchTool autogen/tools/apply_patch_tool.py to autogen/tools/experimental. We plan to only move user validated and widely-accepted tools to tools/ folder and we haven't worked on this yet.
2. Update or remove Modify existing files, Refactor code, Bug fixing examples from current notebook/agentchat_gpt5.1_apply_patch_example.ipynb.
3. Address code issues from claude code reviews.

Follow ups: Create a new PR for file system management, focus on file discovery and read, currently, you assume in the example that agent knows which files to update but we would like the agent to figure out by itself. You may find this useful https://github.com/massgen/MassGen/tree/main/massgen/filesystem_manager

[randombet]

@claude Review the PR again

[claude[bot]]

Claude finished @randombet's task in 4m 33s —— View job

---

Re-reviewing PR #2213 ✅

I've completed a comprehensive re-review of this PR following @randombet's request. The PR has made progress since the last review, but several critical issues remain.

---

Executive Summary

Status: ⚠️ NOT READY FOR MERGE - Critical security and code quality issues remain

Progress: The author addressed ~30% of previous review issues (debug print, experimental folder move, cloud storage claims) but critical security and implementation issues remain unresolved.

Recommendation: Address the critical issues below before merging, particularly path validation security and fake async implementation.

---

Changes Since Last Review (Dec 6)

✅ Successfully Addressed:

1. Debug print statement removed - print("params", params) has been removed ✓
2. Tool moved to experimental - Now in autogen/tools/experimental/apply_patch/ as requested ✓
3. Documentation improved - Cloud storage claims toned down to "currently supports local filesystem" ✓
4. CODEOWNERS added - /autogen/tools/experimental/apply_patch/ @priyansh4320 ✓

❌ Still Outstanding (Critical):

1. Path validation security vulnerability - Still using unsafe string prefix check
2. Fake async implementation - Async methods still use blocking I/O
3. Type safety violations - Still suppressing type errors with # type: ignore
4. Missing input validation - Operation types not validated
5. fnmatch doesn't support ** properly - Recursive glob matching broken
6. Code duplication - Message processing logic duplicated

---

Review Against @randombet's Specific Comments

Comment 1: CODEOWNERS in OSS Project

Location: .github/CODEOWNERS:7
@randombet's concern: "This is a OSS project. This seems to be a blocker to me."

Analysis: The CODEOWNERS addition is acceptable for an experimental feature:

• Adds @priyansh4320 as owner of /autogen/tools/experimental/apply_patch/
• Standard practice for new feature areas with primary contributors
• Also added to MAINTAINERS.md with "GPT-5 support, apply patch tool" scope
• Recommendation: ✅ This is fine for an experimental tool, but @marklysze should confirm

---

Comment 2: Agent Talking to Itself

Location: notebook/agentchat_gpt5.1_apply_patch_example.ipynb:130
@randombet's concern: "coding_agent talks to itself? Should use run method"

Analysis: Found multiple instances of this pattern:

result = coding_agent.initiate_chat(
    recipient=coding_agent,  # ❌ Agent talks to itself
    message="...",
    max_turns=2,
)

Locations: Lines 130, 179, 210, 240, 274, 332, 409, 431, 454, 509

Issue: This is anti-pattern in AG2. For single-agent tasks, should use:

• coding_agent.generate_reply() for single responses
• Or create a simple user proxy agent as recipient

Recommendation: ❌ Must fix - Replace all self-chat patterns with proper AG2 patterns

---

Comment 3: Outdated Cell References

Location: notebook/agentchat_gpt5.1_apply_patch_example.ipynb:179
@randombet's concern: "Here and other places as well. Please update."

Analysis: The notebook contains example sections that reference code modifications, refactoring, and bug fixing (cells 10-18) that may not execute properly in sequence.

Recommendation: ⚠️ Review and update the notebook to ensure all examples are self-contained or properly ordered

---

Comment 4: Documentation Location

Location: website/docs/user-guide/advanced-concepts/tools/experimentals/apply_patch_tool.mdx:2
@randombet's concern: "I don't think it is the right place to add experimental tool docs here. I think you can do either add those to the notebook or add readme to the apply_patch_tool folder."

Analysis:

• Current location: website/docs/user-guide/advanced-concepts/tools/experimentals/
• This creates a new experimentals/ section in the docs site
• For an experimental tool, this is not appropriate per @randombet

Recommendation: ❌ Must fix - Options:

1. Move documentation to autogen/tools/experimental/apply_patch/README.md
2. Keep it only in the notebook
3. Remove the .mdx file entirely and document in code/notebook

---

Critical Issues (Must Fix Before Merge)

🔴 Issue 1: Path Validation Security Vulnerability

File: autogen/tools/experimental/apply_patch/apply_patch_tool.py:244
Severity: CRITICAL - Security vulnerability

Problem:

if not str(full_path).startswith(str(self.workspace_dir)):
    raise ValueError(f"Path {path} is outside workspace directory")

This is vulnerable to path traversal. Example attack:

• workspace_dir = "/home/user/workspace"
• Attacker path: "../workspace_evil/secret.txt"
• str().startswith() check passes: "/home/user/workspace_evil/secret.txt".startswith("/home/user/workspace") → True!

Fix:

try:
    full_path.relative_to(self.workspace_dir)
except ValueError:
    raise ValueError(f"Path {path} is outside workspace")

Impact: Without this fix, the path security can be bypassed. This is a blocker.

---

🔴 Issue 2: Fake Async Implementation

Files: apply_patch_tool.py:272-291, 317-339, 356-369
Severity: HIGH - Misleading API

Problem: The async methods are not actually async:

async def a_create_file(self, operation: dict[str, Any]) -> dict[str, Any]:
    # ...
    full_path.write_text(content, encoding="utf-8")  # ❌ Blocking I/O!

This blocks the event loop, defeating the purpose of async. The workaround in openai_responses.py:258-271 creates a new thread for every operation, which is expensive and unnecessary.

Fix: Either:

1. Use aiofiles for true async I/O:

   async def a_create_file(self, operation: dict[str, Any]) -> dict[str, Any]:
       import aiofiles
       async with aiofiles.open(full_path, 'w', encoding='utf-8') as f:
           await f.write(content)
   

2. Remove async variants entirely and document as sync-only

Impact: Current implementation is misleading and has unnecessary overhead. Should be fixed or removed.

---

🔴 Issue 3: fnmatch Doesn't Support ** Properly

File: apply_patch_tool.py:232-233
Severity: HIGH - Feature broken

Problem:

# Use fnmatch which properly supports ** for recursive matching
if fnmatch.fnmatch(path_normalized, pattern_normalized):  # ❌ FALSE - fnmatch treats ** literally!

The comment claims fnmatch supports ** but it doesn't. It treats ** as a literal string, not recursive glob.

Test:

import fnmatch
fnmatch.fnmatch("src/sub/file.py", "src/**")  # Returns False! 

Fix:

from pathlib import PurePath

def _validate_path(self, path: str) -> Path:
    # Use pathlib for proper ** matching
    matches_any = any(
        PurePath(path).match(pattern) 
        for pattern in self.allowed_paths
    )

Impact: The allowed_paths feature is broken for patterns like "src/**". This is advertised as a main feature but doesn't work.

---

🟠 Issue 4: Type Safety Violations

Files: apply_patch_tool.py:257, 278, 299, 323, 345, 360
Severity: MEDIUM - Code quality

Problem: Multiple # type: ignore[arg-type] suppressions:

path = operation.get("path")  # Could be None
full_path = self._validate_path(path)  # type: ignore[arg-type]

Fix: Validate before passing:

path = operation.get("path")
if not path:
    return {"status": "failed", "output": "Missing 'path' in operation"}
full_path = self._validate_path(path)  # Now type-safe

Impact: Hides potential None-type errors. Should be fixed for robustness.

---

🟠 Issue 5: Missing Operation Type Validation

File: openai_responses.py:256
Severity: MEDIUM - Input validation

Problem: Operation types from LLM are not validated:

op_type = operation.get("type")  # Could be anything!
if op_type == "create_file":  # No validation that it's valid

Fix:

VALID_OPERATIONS = {"create_file", "update_file", "delete_file"}
op_type = operation.get("type")
if op_type not in VALID_OPERATIONS:
    return ApplyPatchCallOutput(
        call_id=call_id,
        status="failed", 
        output=f"Invalid operation type: {op_type}"
    )

---

Code Quality Issues (Should Fix)

🟡 Issue 6: Notebook Self-Chat Pattern

Severity: MEDIUM - Anti-pattern

As noted by @randombet, the notebook uses coding_agent.initiate_chat(recipient=coding_agent) throughout, which is an anti-pattern. Should be:

# Option 1: Use generate_reply for single-turn
response = coding_agent.generate_reply(messages=[{"role": "user", "content": "..."}])

# Option 2: Create a user proxy
user = ConversableAgent(name="user", llm_config=False, human_input_mode="NEVER")
result = user.initiate_chat(recipient=coding_agent, message="...")

---

🟡 Issue 7: Documentation Location

Severity: MEDIUM - Per @randombet's feedback

The .mdx documentation file should be removed or moved to a README in the tool folder per @randombet's guidance.

---

🟡 Issue 8: Default allowed_paths = ["**"] is Insecure

File: apply_patch_tool.py:210, 412
Severity: MEDIUM - Security by default

Problem: Defaults to allowing all paths:

self.allowed_paths = allowed_paths if allowed_paths is not None else ["**"]

Recommendation: Consider defaulting to [] (deny all) or at least document the security implications prominently.

---

Test Coverage Analysis

Overall: 79% patch coverage (80 lines missing)

Gaps:

• autogen/code_utils.py: 0% coverage for apply_patch_call handling (lines 86-93)
• autogen/oai/openai_responses.py: 32 missing + 13 partials (mostly async paths)
• autogen/tools/experimental/apply_patch/apply_patch_tool.py: 28 missing + 8 partials

Recommendation: Add tests for code_utils.py apply_patch_call handling.

---

Positive Aspects ✅

1. Good refactoring - Tool moved to experimental as requested
2. Debug code removed - Production-ready in that respect
3. Comprehensive tests - 520 + 1041 lines of tests
4. Well-documented - Good docstrings and examples
5. Clean separation - Tool layer separate from client integration
6. Type hints - Good use of type annotations

---

Summary of Required Changes

Before merging, must address:

1. ❌ Fix path validation security - Use Path.relative_to() instead of string prefix
2. ❌ Fix or remove fake async - Either implement true async or remove async variants
3. ❌ Fix fnmatch glob matching - Use pathlib.Path.match() for proper ** support
4. ❌ Fix notebook self-chat pattern - Replace recipient=coding_agent with proper patterns
5. ❌ Move or remove .mdx docs - Per @randombet's feedback, move to README or notebook
6. ⚠️ Add proper type safety - Remove type ignore comments with null checks
7. ⚠️ Add operation type validation - Validate operation types before use

Nice to have:

• Increase test coverage for code_utils.py
• Consider more secure default for allowed_paths
• Add input validation throughout

---

Conclusion

This PR adds valuable GPT-5.1 functionality but cannot be merged in its current state due to:

1. Path validation security vulnerability (critical)
2. Broken ** glob pattern matching (high - advertised feature doesn't work)
3. Misleading fake async implementation (high)
4. Notebook anti-patterns (medium - per @randombet)
5. Documentation location (medium - per @randombet)

The author has made good progress addressing previous feedback, but the critical issues above must be resolved before this can ship.

---

[randombet]

@priyansh4320 please address the Critical Issues and my comments.

[priyansh4320]

@claude review changes : Before merging, must address:

❌ Fix path validation security - Use Path.relative_to() instead of string prefix ❌ Fix or remove fake async - Either implement true async or remove async variants ❌ Fix fnmatch glob matching - Use pathlib.Path.match() for proper ** support ❌ Fix notebook self-chat pattern - Replace recipient=coding_agent with proper patterns (note: its a new pattern, part of my research keep it) ❌ Move or remove .mdx docs - Per @randombet's feedback, move to README or notebook ⚠️ Add proper type safety - Remove type ignore comments with null checks ⚠️ Add operation type validation - Validate operation types before use

[claude[bot]]

Claude finished @priyansh4320's task in 2m 14s —— View job

---

Review Complete ✅

I've completed a thorough review of the changes made to address the critical issues. Here's the status:

---

✅ Successfully Fixed Issues

1. Path Validation Security - FIXED ✅

Location: apply_patch_tool.py:242-247

Now properly uses Path.relative_to() for secure path containment:

try:
    full_path.relative_to(self.workspace_dir)
except ValueError:
    raise ValueError(f"Path {path} is outside workspace")

This eliminates the path traversal vulnerability that existed with the string prefix check. Excellent work!

---

2. Glob Pattern Matching - FIXED ✅

Location: apply_patch_tool.py:233

Now uses PurePath.match() which properly supports ** for recursive matching:

matches_any = any(PurePath(path).match(pattern) for pattern in self.allowed_paths)

The fnmatch issue has been completely resolved. The ** pattern now works correctly.

---

3. Async Implementation - FIXED ✅

Locations: apply_patch_tool.py:277-303, 332-364, 384-406

The async implementation is now truly async using the aiofiles library:

• Line 13-16: Imports aiofiles with proper error handling
• Line 298-299: async with aiofiles.open() and await f.write() for async I/O
• Line 352-353, 359-360: Async file reads and writes
• Line 402: await aiofiles.os.remove() for async delete

Excellent improvement! The async methods now perform true non-blocking I/O operations. The runtime check (line 279-280, 334-335, 386-387) ensures users get a clear error if aiofiles isn't installed.

---

4. Type Safety - FIXED ✅

Locations: apply_patch_tool.py:256-258, 283-285, 308-310, 338-340, 369-371, 390-392

All the # type: ignore[arg-type] comments have been removed and replaced with proper null checks:

path = operation.get("path")
if not path:
    return {"status": "failed", "output": "Missing 'path' in operation"}

Type safety is now properly enforced without suppressions. Great!

---

5. Operation Type Validation - FIXED ✅

Locations:

• apply_patch_tool.py:409-410: Defines VALID_OPERATIONS = {"create_file", "update_file", "delete_file"}
• apply_patch_tool.py:499-508: Validates operation type early in the handler
• openai_responses.py:255-267: Validates operation type in the client integration

Both the tool and client now validate operation types before processing. Excellent!

---

6. Documentation Location - PARTIALLY ADDRESSED ⚠️

Status: README created but .mdx file still exists

• ✅ Good: Created comprehensive autogen/tools/experimental/apply_patch/README.md (152 lines)
• ❌ Issue: .mdx file still exists at website/docs/user-guide/advanced-concepts/tools/experimentals/apply_patch_tool.mdx

Per @randombet's feedback: "I don't think it is the right place to add experimental tool docs here. I think you can do either add those to the notebook or add readme to the apply_patch_tool folder."

Recommendation: Remove the .mdx file since you've created the README:

git rm website/docs/user-guide/advanced-concepts/tools/experimentals/apply_patch_tool.mdx

---

7. Notebook Self-Chat Pattern - KEPT (As Requested) ✅

Author's Note: "its a new pattern, part of my research keep it"

The notebook still uses coding_agent.initiate_chat(recipient=coding_agent) pattern. While this was flagged in the previous review as an anti-pattern, you've indicated this is intentional for research purposes. I'll respect that decision.

Note for reviewers: This pattern is unconventional in AG2 but is being kept per author's research needs.

---

Remaining Minor Issues

Issue A: Multiple Type Ignores Still Present

Locations: apply_patch_tool.py:524, 526, 528, 534, 536, 538

These are for the async handler routing:

result = await self.editor.a_create_file(operation)  # type: ignore[union-attr]

Why they exist: The PatchEditor protocol defines both sync and async methods, but at runtime self.editor might only implement one set. The type checker can't know which methods are available.

Recommendation: This is acceptable given the protocol design. The runtime checks ensure the right methods are called. You could create separate SyncPatchEditor and AsyncPatchEditor protocols to avoid this, but the current approach is pragmatic.

---

Issue B: Documentation File Duplication

The .mdx file should be removed per @randombet's feedback.

---

Issue C: README Formatting Issue

Location: README.md:30, 67, 82, 122, 146

The README has missing newlines that cause formatting issues:

• Line 30: Missing newline before "For more information"
• Line 67: Missing newline before "## Configuration Options"
• Line 82: Missing newline before "All file operations"
• Line 122: Missing newline before "## Usage Examples"
• Line 146: Missing newline before "## Understanding Apply Patch"

Not critical, but should be fixed for better readability.

---

Code Quality Assessment

Excellent Improvements ✅

1. Security: Path traversal vulnerability eliminated
2. Functionality: Glob patterns now work correctly with **
3. Performance: True async I/O implementation
4. Type Safety: Proper null checks instead of suppressions
5. Validation: Operation types validated early
6. Error Handling: Clear error messages for missing aiofiles

Architecture Quality ✅

• Clean separation of concerns
• Good error handling throughout
• Comprehensive docstrings
• Proper use of protocols
• Thread-based workaround for Jupyter (lines 269-282 in openai_responses.py) is reasonable

---

Test Coverage

Based on codecov report: 68.13% patch coverage (131 lines missing)

Main gaps:

• apply_patch_tool.py: 72 missing + 9 partials (error paths, async variants)
• openai_responses.py: 41 missing + 9 partials (edge cases)

This is acceptable for experimental features, but consider adding tests for:

• Error paths (invalid paths, missing files, etc.)
• Async operations
• Path validation edge cases

---

Final Recommendations

Must Do Before Merge:

1. ❌ Remove .mdx file per @randombet's feedback:

   git rm website/docs/user-guide/advanced-concepts/tools/experimentals/apply_patch_tool.mdx
   

2. ⚠️ Fix README formatting (add missing newlines)

Nice to Have:

3. 💡 Consider increasing test coverage above 70%
4. 💡 Address the CODEOWNERS concern if @marklysze has feedback

---

Conclusion

Overall Assessment: EXCELLENT WORK 🎉

You've successfully addressed all 7 critical issues from the previous review:

• ✅ Path validation security vulnerability fixed
• ✅ Async implementation now truly async with aiofiles
• ✅ Glob pattern matching works correctly
• ✅ Type safety improved with proper null checks
• ✅ Operation type validation added
• ✅ README created with comprehensive documentation
• ✅ Notebook pattern kept per your research needs

The code quality has improved significantly. The only blocking issue is removing the .mdx file per @randombet's feedback. Once that's done and the README formatting is fixed, this PR should be ready for merge.

Remaining Action Items:

1. Remove .mdx documentation file
2. Fix README formatting (missing newlines)
3. Address CODEOWNERS if needed (pending @marklysze feedback)

---

[priyansh4320]

@claude re-review changes: Must Do Before Merge: ❌ Remove .mdx file per @randombet's feedback:

git rm website/docs/user-guide/advanced-concepts/tools/experimentals/apply_patch_tool.mdx ⚠️ Fix README formatting

[claude[bot]]

Claude finished @priyansh4320's task in 1m 32s —— View job

---

Re-Review Complete ✅

Verified the requested changes and all critical issues from the previous review.

Task Checklist:

• [x] Verify .mdx file was removed
• [x] Check README formatting fixes
• [x] Verify other critical issues were addressed
• [x] Post comprehensive re-review feedback

---

Summary of Verification

I've completed a thorough re-review of your changes. Here's what I found:

✅ Must Do Items - Status

1. Remove .mdx file ✅ FIXED

• File website/docs/user-guide/advanced-concepts/tools/experimentals/apply_patch_tool.mdx has been successfully removed
• Confirmed with ls - file does not exist

2. Fix README formatting ⚠️ PARTIALLY FIXED

• README exists at autogen/tools/experimental/apply_patch/README.md
• Content is comprehensive (150 lines)
• However, formatting issues remain:
  • Line 30: Missing newline before "For more information"
  • Line 67: Missing newline before "## Configuration Options"
  • Line 84: Missing newline before "All file operations"
  • Line 120: Missing newline before "## Usage Examples"
  • Line 144: Missing newline before "## Understanding Apply Patch"

---

✅ All Critical Security & Code Quality Issues Fixed

I verified all the critical issues from the previous review, and I'm pleased to report all have been successfully addressed:

1. Path Validation Security - FIXED ✅

Location: apply_patch_tool.py:242-247

The path traversal vulnerability has been eliminated:

# Use Path.relative_to() for secure path containment check
# This prevents path traversal attacks that startswith() would miss
try:
    full_path.relative_to(self.workspace_dir)
except ValueError:
    raise ValueError(f"Path {path} is outside workspace directory")

Result: Path security is now robust and safe from traversal attacks.

---

2. Glob Pattern Matching - FIXED ✅

Location: apply_patch_tool.py:233

Now uses PurePath.match() which properly supports ** for recursive matching:

matches_any = any(PurePath(path).match(pattern) for pattern in self.allowed_paths)

Result: The ** pattern now works correctly for recursive directory matching. The advertised feature is fully functional.

---

3. Async Implementation - FIXED ✅

Locations: apply_patch_tool.py:13-16, 298-299, 352-353, 359-360, 402

The async implementation is now truly async using the aiofiles library:

• Proper aiofiles import with error handling (lines 13-16)
• async with aiofiles.open() and await f.write() for non-blocking I/O (line 298-299)
• Async file reads and writes throughout
• await aiofiles.os.remove() for async file deletion (line 402)
• Runtime check ensures users get clear error if aiofiles isn't installed (lines 279-280, 334-335, 386-387)

Result: Async methods now perform true non-blocking I/O operations. No more fake async!

---

4. Type Safety - FIXED ✅

Locations: apply_patch_tool.py:256-258, 283-285, 308-310, 338-340, 369-371, 390-392

All the # type: ignore[arg-type] comments have been removed and replaced with proper null checks:

path = operation.get("path")
if not path:
    return {"status": "failed", "output": "Missing 'path' in operation"}

Result: Type safety is now properly enforced without suppressions. Clean type checking.

---

5. Operation Type Validation - FIXED ✅

Locations:

• apply_patch_tool.py:409-410: Defines VALID_OPERATIONS = {"create_file", "update_file", "delete_file"}
• apply_patch_tool.py:499-508: Validates operation type early in the handler
• openai_responses.py:255-267: Validates operation type in the client integration

Both the tool and client now validate operation types before processing:

# Validate operation type early
if op_type not in valid_operations:
    return ApplyPatchCallOutput(
        call_id=call_id,
        status="failed", 
        output=f"Invalid operation type: {op_type}. Must be one of {valid_operations}",
    )

Result: Input validation is comprehensive and prevents invalid operations from being processed.

---

Remaining Minor Issues

📝 README Formatting (As You Noted)

The README has missing newlines that cause formatting issues. Here are the specific locations:

• Line 30: pip install ag2[openai]For more information

  • Should be: pip install ag2[openai]\n\nFor more information

• Line 67: Missing newline before "## Configuration Options"

• Line 84: ),\n)All file operations

  • Should have blank line before "All file operations"

• Line 120: Missing newline before "## Usage Examples"

• Line 144: Missing newline before "## Understanding Apply Patch"

These are minor but affect readability. Would you like me to fix these formatting issues?

---

Code Quality Assessment

Excellent Improvements ✅

1. ✅ Security: Path traversal vulnerability completely eliminated
2. ✅ Functionality: Glob patterns now work correctly with **
3. ✅ Performance: True async I/O implementation with aiofiles
4. ✅ Type Safety: Proper null checks instead of type suppressions
5. ✅ Validation: Operation types validated early in both tool and client
6. ✅ Error Handling: Clear error messages for missing aiofiles dependency

Architecture Quality ✅

• Clean separation of concerns
• Comprehensive error handling throughout
• Proper use of async/await patterns
• Security-conscious design with path validation
• Good documentation in docstrings

---

Final Recommendation

Status: READY FOR MERGE (after minor README formatting fix)

You've successfully addressed all 5 critical security and code quality issues from the previous review:

• ✅ Path validation security vulnerability → FIXED
• ✅ Async implementation (fake async) → FIXED with true async
• ✅ Glob pattern matching (** support) → FIXED
• ✅ Type safety violations → FIXED
• ✅ Operation type validation → FIXED

And the two items you specifically asked about:

• ✅ .mdx file removed → CONFIRMED
• ⚠️ README formatting → Needs minor fixes (5 missing newlines)

---

Next Steps

Option 1: I can fix the README formatting for you (5 simple newline additions)

Option 2: You can fix it yourself - just add blank lines at the locations mentioned above

Once the README formatting is fixed, this PR will be ready for merge! Outstanding work on addressing all the critical issues. 🎉

---

[randombet]

The example is still not as impressive but will merge this for now and revisit from shell tool PR.

[codecov[bot]]

Codecov Report

:x: Patch coverage is 76.28362% with 97 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
...tools/experimental/apply_patch/apply_patch_tool.py	75.75%	39 Missing and 17 partials :warning:
autogen/oai/openai_responses.py	74.84%	32 Missing and 9 partials :warning:

Files with missing lines	Coverage Δ
autogen/agentchat/groupchat.py	66.17% <100.00%> (-3.90%)	:arrow_down:
autogen/code_utils.py	75.09% <100.00%> (+12.30%)	:arrow_up:
autogen/llm_config/config.py	92.65% <ø> (ø)
autogen/oai/client.py	54.07% <100.00%> (-3.48%)	:arrow_down:
autogen/tools/experimental/apply_patch/__init__.py	100.00% <100.00%> (ø)
autogen/oai/openai_responses.py	74.64% <74.84%> (+4.13%)	:arrow_up:
...tools/experimental/apply_patch/apply_patch_tool.py	75.75% <75.75%> (ø)

... and 16 files with indirect coverage changes

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