Significant input lag on first prompt submission in large project directories (Windows 11)

Description

Claude Code v2.1.87 on Windows 11 exhibits a noticeable freeze/block when submitting the first prompt in a large project directory. The user can type freely, but pressing Enter causes the client to become non-interactive for several seconds before the prompt is processed.

The lag does not occur when launching Claude Code from ~/.claude/ (a small directory) — only from a large project directory (Unreal Engine 5 project, ~hundreds of thousands of files).

Environment

• OS: Windows 11 Home 10.0.26200
• Claude Code version: 2.1.87
• Shell: Git Bash
• Auth: Claude Max (OAuth)
• Project: Large Unreal Engine 5 codebase (Perforce, not Git)

Reproduction

1. cd into a large project directory
2. Run claude
3. Type any prompt and press Enter
4. Observe: the client freezes for several seconds before processing

Compare with:

1. cd ~/.claude
2. Run claude
3. Type any prompt and press Enter
4. Observe: near-instant response

Systematic investigation performed

The following were each disabled/removed individually and in combination — none resolved the issue:

| What was disabled | Result |
|---|---|
| All plugins (bootstrap@plugins-kit, unreal-kit@plugins-kit, update@update06) set to false | Still slow |
| Remote Control for all sessions (via /config) | Still slow |
| SessionStart hooks (emptied) | Still slow |
| Plugin UserPromptSubmit hooks (emptied from plugin cache hooks.json) | Still slow |
| MCP servers (removed unreal-engine from enabledMcpjsonServers) | Still slow |
| claude --bare (skips hooks, LSP, plugin sync, attribution, auto-memory, prefetches, keychain, CLAUDE.md) | Still slow |
| Replaced settings.json with minimal {"permissions":{"defaultMode":"acceptEdits"}} | Still slow |
| Renamed .mcp.json out of the way | Still slow |
| Renamed entire .claude/ directory (replaced with empty dir + minimal settings.json) | Still slow |

The lag persists even with --bare and a completely empty .claude/ directory containing only a minimal settings.json. The only factor that correlates with the lag is the CWD being a large project directory vs a small one.

Question

Is there an automated filesystem scanning or discovery process (file indexing, gitignore/ignore-file discovery, file suggestion indexing, etc.) that runs on startup or first prompt submission? In a large project directory with hundreds of thousands of files, this could explain the observed latency.

Expected behavior

Submitting a prompt should be near-instant regardless of project directory size, or any scanning should be non-blocking.

🤖 Generated with Claude Code