[Bug] Subagents unable to write files and call MCP tools silently

Bug Description

Bug Report: Subagents Cannot Write Files or Call MCP Tools (Silent Failures)

Summary

Subagents spawned via the Task tool have lost the ability to write files and call MCP tools. These failures are silent - the subagent believes the operation succeeded, but nothing actually happens. The main conversation agent can perform these operations successfully.

Environment

OS: macOS (Darwin 24.6.0)
Claude Code Version: 2.0.68
Date Issue Started: December 12-13, 2025 (overnight)

Reproduction Steps

Issue 1: Write Tool Silent Failure

Start a conversation with Claude Code

Spawn a background subagent:

Task tool with:

• subagent_type: "general-purpose"
• run_in_background: true
• prompt: "Create a file at ./test-subagent-write.md with the content 'Hello World'"

Wait for subagent to complete

Check if file exists: ls -la ./test-subagent-write.md

Expected: File is created
Actual: File does NOT exist, but subagent reports success

Issue 2: MCP Tool Call Failure

Create a subagent with MCP tools in its tools list:

tools:

• Read
• mcp__some-server__some_tool

Spawn the subagent via Task tool

Instruct it to call the MCP tool

Expected: MCP tool is called
Actual: Subagent fails to call MCP tool (may skip it or error)

Workaround

For Write tool: Have subagents return content to main agent, which then writes files.
For MCP tools: No known workaround - must use main agent directly.

Additional Notes

This appears to be a regression - both features worked before December 12-13, 2025
Failures are silent making debugging extremely difficult
Affects both run_in_background: true and potentially foreground subagents
May be related to sandboxing/permission changes in a recent Claude Code update

Environment Info

• Platform: darwin
• Terminal: ghostty
• Version: 2.0.68
• Feedback ID: fe203b0c-8eee-4427-9ec0-4a00cbf9b2a2