[Bug] Incomplete Commit: Partial Staging Instead of Full Repository Commit

Bug Description
when asked to do a full commmit of everything only partially commits!

Environment Info

• Platform: win32
• Terminal: null
• Version: 1.0.90
• Feedback ID: d833461f-6f66-4565-8bf8-07f541a5e7a7

Errors

[{"error":"Error: Failed to install new version of claude:  npm error code EBUSY\nnpm error syscall copyfile\nnpm error path C:\\Users\\Jeremy.VanRyswyk\\AppData\\Roaming\\npm\\node_modules\\@anthropic-ai\\claude-code\\node_modules\\@img\\sharp-win32-x64\\lib\\libvips-cpp.dll\nnpm error dest C:\\Users\\Jeremy.VanRyswyk\\AppData\\Roaming\\npm\\node_modules\\@anthropic-ai\\.claude-code-5UOYNWyD\\node_modules\\@img\\sharp-win32-x64\\lib\\libvips-cpp.dll\nnpm error errno -4082\nnpm error EBUSY: resource busy or locked, copyfile 'C:\\Users\\Jeremy.VanRyswyk\\AppData\\Roaming\\npm\\node_modules\\@anthropic-ai\\claude-code\\node_modules\\@img\\sharp-win32-x64\\lib\\libvips-cpp.dll' -> 'C:\\Users\\Jeremy.VanRyswyk\\AppData\\Roaming\\npm\\node_modules\\@anthropic-ai\\.claude-code-5UOYNWyD\\node_modules\\@img\\sharp-win32-x64\\lib\\libvips-cpp.dll'\nnpm error A complete log of this run can be found in: C:\\Users\\Jeremy.VanRyswyk\\AppData\\Local\\npm-cache\\_logs\\2025-08-26T01_57_39_721Z-debug-0.log\n    at N31 (file:///C:/Users/Jeremy.VanRyswyk/AppData/Roaming/npm/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:///C:/Users/Jeremy.VanRyswyk/AppData/Roaming/npm/node_modules/@anthropic-ai/claude-code/cli.js:3434:10962","timestamp":"2025-08-26T01:57:40.882Z"},{"error":"Error: Command failed: C:\\Users\\Jeremy.VanRyswyk\\AppData\\Roaming\\npm\\node_modules\\@anthropic-ai\\claude-code\\vendor\\ripgrep\\x64-win32\\rg.exe --hidden -n REMOVED_FALLBACK C:\\Users\\Jeremy.VanRyswyk\\source\\repos\\plan-maker\nrg: C:\\Users\\Jeremy.VanRyswyk\\source\\repos\\plan-maker\\nul: Incorrect function. (os error 1)\nrg: C:\\Users\\Jeremy.VanRyswyk\\source\\repos\\plan-maker\\.vs\\Plan Maker\\FileContentIndex\\2855e141-5c35-40ef-bbff-bbc4e3fdcf00.vsidx: The process cannot access the file because it is being used by another process. (os error 32)\nrg: C:\\Users\\Jeremy.VanRyswyk\\source\\repos\\plan-maker\\.vs\\Plan Maker\\FileContentIndex\\3f8a373b-2da4-4c9a-b502-1e9da8aac066.vsidx: The process cannot access the file because it is being used by another process. (os error 32)\nrg: C:\\Users\\Jeremy.VanRyswyk\\source\\repos\\plan-maker\\.vs\\Plan Maker\\FileContentIndex\\716f832e-f137-4e15-a318-aacca8c53e01.vsidx: The process cannot access the file because it is being used by another process. (os error 32)\nrg: C:\\Users\\Jeremy.VanRyswyk\\source\\repos\\plan-maker\\.vs\\Plan Maker\\FileContentIndex\\8d384543-2b22-4ef8-a1d7-9105cd39d58f.vsidx: The process cannot access the file because it is being used by another process. (os error 32)\nrg: C:\\Users\\Jeremy.VanRyswyk\\source\\repos\\plan-maker\\.vs\\Plan Maker\\FileContentIndex\\e0ccc82e-93d5-4359-9079-b42f8dc22260.vsidx: The process cannot access the file because it is being used by another process. (os error 32)\n\n    at genericNodeError (node:internal/errors:983:15)\n    at wrappedFn (node:internal/errors:537:14)\n    at ChildProcess.exithandler (node:child_process:415:12)\n    at ChildProcess.emit (node:events:518:28)\n    at ChildProcess.emit (node:domain:489:12)\n    at maybeClose (node:internal/child_process:1101:16)\n    at ChildProcess._handle.onexit (node:internal/child_process:304:5)","timestamp":"2025-08-26T02:15:07.625Z"},{"error":"Error: Request was aborted.\n    at HP.makeRequest (file:///C:/Users/Jeremy.VanRyswyk/AppData/Roaming/npm/node_modules/@anthropic-ai/claude-code/cli.js:943:3840)\n    at process.processTicksAndRejections (node:internal/process/task_queues:105:5)","timestamp":"2025-08-26T02:15:08.430Z"},{"error":"Error: 400 {\"type\":\"error\",\"error\":{\"type\":\"invalid_request_error\",\"message\":\"too many total text bytes: 17167269 > 16000000\"},\"request_id\":\"req_011CSVWzn5jRMwAMMqt1m8y8\"}\n    at b4.generate (file:///C:/Users/Jeremy.VanRyswyk/AppData/Roaming/npm/node_modules/@anthropic-ai/claude-code/cli.js:926:2412)\n    at HP.makeStatusError (file:///C:/Users/Jeremy.VanRyswyk/AppData/Roaming/npm/node_modules/@anthropic-ai/claude-code/cli.js:943:2101)\n    at HP.makeRequest (file:///C:/Users/Jeremy.VanRyswyk/AppData/Roaming/npm/node_modules/@anthropic-ai/claude-code/cli.js:943:5314)\n    at process.processTicksAndRejections (node:internal/process/task_queues:105:5)","timestamp":"2025-08-26T02:18:44.549Z"},{"error":"Error: EISDIR: illegal operation on a directory, read\n    at Module.readFileSync (node:fs:441:20)\n    at Object.readFileSync (file:///C:/Users/Jeremy.VanRyswyk/AppData/Roaming/npm/node_modules/@anthropic-ai/claude-code/cli.js:690:9211)\n    at CeA (file:///C:/Users/Jeremy.VanRyswyk/AppData/Roaming/npm/node_modules/@anthropic-ai/claude-code/cli.js:735:9240)\n    at Object.call (file:///C:/Users/Jeremy.VanRyswyk/AppData/Roaming/npm/node_modu

Note: Error logs were truncated.