[Bug] Phantom File Edits: No Actual Changes Persisted

Bug Description
it keeps saying tha tit updated a file or made a new file but those edits are not real

Environment Info

• Platform: darwin
• Terminal: Apple_Terminal
• Version: 1.0.89
• Feedback ID: f86470a1-b835-4c9c-bd0f-4b170e365807

Errors

[{"error":"Error: Failed to install new version of claude:  npm error code ENOTEMPTY\nnpm error syscall rename\nnpm error path /opt/homebrew/lib/node_modules/@anthropic-ai/claude-code\nnpm error dest /opt/homebrew/lib/node_modules/@anthropic-ai/.claude-code-2DTsDk1V\nnpm error errno -66\nnpm error ENOTEMPTY: directory not empty, rename '/opt/homebrew/lib/node_modules/@anthropic-ai/claude-code' -> '/opt/homebrew/lib/node_modules/@anthropic-ai/.claude-code-2DTsDk1V'\nnpm error A complete log of this run can be found in: /Users/rivir/.npm/_logs/2025-10-03T00_40_39_308Z-debug-0.log\n    at L31 (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:1633:392)\n    at process.processTicksAndRejections (node:internal/process/task_queues:105:5)\n    at async file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:3434:10962","timestamp":"2025-10-03T00:40:39.507Z"},{"error":"SyntaxError: Unexpected token 'I', \"I apologiz\"... is not valid JSON\n    at JSON.parse (<anonymous>)\n    at file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:712:9932\n    at Q (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:671:13339)\n    at cn2 (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:1058:1992)\n    at process.processTicksAndRejections (node:internal/process/task_queues:105:5)","timestamp":"2025-10-03T00:41:09.595Z"},{"error":"SyntaxError: Unexpected token 'I', \"I apologiz\"... is not valid JSON\n    at JSON.parse (<anonymous>)\n    at file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:712:9932\n    at Q (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:671:13339)\n    at cn2 (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:1058:1992)\n    at process.processTicksAndRejections (node:internal/process/task_queues:105:5)","timestamp":"2025-10-03T00:41:18.843Z"},{"error":"Error: Failed to install new version of claude:  npm error code ENOTEMPTY\nnpm error syscall rename\nnpm error path /opt/homebrew/lib/node_modules/@anthropic-ai/claude-code\nnpm error dest /opt/homebrew/lib/node_modules/@anthropic-ai/.claude-code-2DTsDk1V\nnpm error errno -66\nnpm error ENOTEMPTY: directory not empty, rename '/opt/homebrew/lib/node_modules/@anthropic-ai/claude-code' -> '/opt/homebrew/lib/node_modules/@anthropic-ai/.claude-code-2DTsDk1V'\nnpm error A complete log of this run can be found in: /Users/rivir/.npm/_logs/2025-10-03T00_47_37_862Z-debug-0.log\n    at L31 (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:1633:392)\n    at process.processTicksAndRejections (node:internal/process/task_queues:105:5)\n    at async file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:3434:10962","timestamp":"2025-10-03T00:47:38.310Z"},{"error":"Error: Failed to install new version of claude:  npm error code ENOTEMPTY\nnpm error syscall rename\nnpm error path /opt/homebrew/lib/node_modules/@anthropic-ai/claude-code\nnpm error dest /opt/homebrew/lib/node_modules/@anthropic-ai/.claude-code-2DTsDk1V\nnpm error errno -66\nnpm error ENOTEMPTY: directory not empty, rename '/opt/homebrew/lib/node_modules/@anthropic-ai/claude-code' -> '/opt/homebrew/lib/node_modules/@anthropic-ai/.claude-code-2DTsDk1V'\nnpm error A complete log of this run can be found in: /Users/rivir/.npm/_logs/2025-10-03T00_47_42_358Z-debug-0.log\n    at L31 (file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:1633:392)\n    at process.processTicksAndRejections (node:internal/process/task_queues:105:5)\n    at async file:///opt/homebrew/lib/node_modules/@anthropic-ai/claude-code/cli.js:3434:10962","timestamp":"2025-10-03T00:47:42.478Z"}]