Claude Desktop auto-updater silently uninstalls Claude Code CLI

Description

Installing Claude Desktop (or its auto-updater ShipIt) silently removes the Claude Code CLI binary at /opt/homebrew/bin/claude and replaces it with Claude Cowork. This breaks any automation that depends on the Claude Code CLI.

Impact

• Heartbeat daemon down: All scheduled tasks stopped running because the claude binary was replaced
• Wrapper scripts broken: Custom wrapper scripts pointing to /opt/homebrew/bin/claude started launching Cowork instead of the CLI
• No warning: No notification, no prompt, no changelog — the binary was silently swapped
• Silent auto-install: The ShipIt auto-updater ran without user consent and modified the global PATH binary

Steps to reproduce

1. Have Claude Code installed via npm install -g @anthropic-ai/claude-code
2. Install Claude Desktop (or let it auto-update)
3. Observe that /opt/homebrew/bin/claude now launches Cowork instead of Claude Code
4. All automation depending on claude CLI breaks

Evidence

ShipIt (Claude Desktop's auto-updater) ran at 5:52 PM and modified the claude-code npm package at 5:50 PM:

~/Library/Caches/com.anthropic.claudefordesktop.ShipIt/ShipIt_stderr.log — updated at 17:52
/opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/ — files modified at 17:50

Expected behavior

• Claude Desktop should NOT modify globally installed CLI tools without explicit user consent
• At minimum: prompt the user before replacing an existing binary
• Ideally: Claude Desktop and Claude Code should coexist without interfering with each other

Workaround

# Reinstall Claude Code via npm
npm install -g @anthropic-ai/claude-code

# Verify
claude --version
# Should show: 2.x.x (Claude Code)

Environment

• macOS Darwin 25.2.0 (ARM64)
• Claude Code 2.1.75 (npm)
• Claude Desktop was installed via .app