CC desktop app: total silence for specific repo, CLI works fine

Description

The Claude Code desktop app produces total silence (no response whatsoever) when a specific repo is selected as the working folder. Any prompt — including simple greetings — results in no output. No error, no spinner, nothing.

The Claude Code CLI works perfectly with the same repo.

Reproduction

• Repo: private GitHub repo (~800KB of markdown reference files, coaching skill system)
• OS: macOS (Darwin 25.3.0)
• Path: /Users/emanuele/Documents/Personal projects/interview-coach-skill-main
• CC desktop app: total silence on any prompt
• CC CLI (claude in terminal, same working directory): works correctly

Timeline

The issue started randomly on 2026-04-01 with no apparent trigger — no code changes, no CC update noticed, no OS changes. The repo had been working fine for months prior.

What I tried

All of the following failed to fix the issue:

1. Full config wipe — deleted all Claude config files, cache, and restarted. Still silent.
2. Removed CLAUDE.md — renamed to .bak so the app had no project instructions. Still silent.
3. Created .claudeignore — excluded references/ (680KB of markdown) and other large files from auto-context. Still silent.
4. Removed .claude/settings.json — the only project-level file that survived the config wipe. Still silent.
5. Cleaned up stale git worktrees — removed 5 orphaned worktree directories and pruned a broken git worktree reference. Removed extensions.worktreeConfig from .git/config. Still silent.
6. Tested via symlink without space in path — created a symlink to eliminate the space in "Personal projects" as a cause. Still silent.
7. Other repos — CC desktop app works normally with all other repos on the same machine.

Expected behavior

The CC desktop app should respond to prompts the same way the CLI does.

Hypothesis

The app likely maintains a per-project state or index in its own internal database, separate from ~/.claude/, that is not cleared by a full config wipe. If that internal record became corrupted for this specific repo, it would cause a silent failure on every message — which would explain why wiping all user-visible config has no effect.