MCP tool calls prompt for permission despite bypass-all permission mode

Description

With permissions set to bypass all, MCP tool calls (e.g., YouTrack MCP server tools like mcp__youtrack__get_article) still trigger permission prompts. Non-MCP tools (Bash, Read, Write, Edit) correctly bypass without prompting.

Steps to Reproduce

1. Set permission mode to bypass all (or equivalent allow-all setting)
2. Make a call to an MCP server tool (e.g., mcp__youtrack__get_article)
3. Permission prompt appears despite bypass-all being active

Expected Behavior

MCP tool calls should respect the bypass-all permission mode and execute without prompting, same as built-in tools.

Observed Behavior

MCP tools still prompt for permission. User has to manually approve each MCP call even though all other tools bypass automatically.

Environment

• Claude Code CLI on macOS (Darwin 25.5.0)
• Model: claude-opus-4-6 (1M context)
• MCP server: YouTrack (via mcp__youtrack__* tools)