Migrate permission system from MCP file-based to stdio-based

Replace MCP permission server with stdio-based permission flow that
communicates directly with Claude CLI via stdin/stdout. This simplifies
the architecture and fixes permission expiration issues.

Key changes:
- Use --permission-prompt-tool stdio and --input-format stream-json
- Handle control_request messages for permission prompts
- Send control_response via stdin to approve/deny
- Check local permissions for auto-approval of pre-approved tools
- Only expire pending permissions when VS Code restarts, not panel close

🤖 Generated with [Claude Code](https://claude.com/claude-code)

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

.vscodeignore

@@ -11,4 +11,6 @@ vsc-extension-quickstart.md
 **/.vscode-test.*
 backup
 .claude
-claude-code-chat-permissions-mcp/**
+claude-code-chat-permissions-mcp/**
+node_modules
+mcp-permissions.js