Claude Code asked to "clean up scaffolding" deleted 2,229 untracked source files from a year-long OS project (GitHub #23913)

1. Instruction given

   Clean up all the scaffolding from a custom operating system project — a subset of files generated by a Python build script.

2. Expected behavior

   Remove the generated scaffolding files the build script had produced and leave the rest of the project — hand-written source, libraries, and documentation — untouched.

3. Actual behavior

   Claude Code ran a PowerShell `Get-ChildItem -Recurse | Remove-Item -Force` sweep and `rm -rf` across roughly 200 directories, deleting every file matching the project's custom source extension system-wide rather than the narrower set of build-generated scaffolding the user meant. Both commands bypass the Windows Recycle Bin, and no confirmation was requested before they ran.

4. Damage

   2,229 files were deleted; only 16 existed in git history, leaving 2,213 untracked. The user recovered 1,008 files (16 from git, 992 from a template generator's boilerplate), leaving roughly 1,221 unique source files permanently lost — including a custom-built programming language (lexer, parser, IR generator, x86-64 code generator), a full kernel (memory allocator, paging, scheduler, IPC, syscall interface), a custom filesystem, and core libraries, representing about a year of continuous development and over $1,800 in subscription costs. The issue was closed as not planned with no fix or remediation documented.

Classification

Agent

Claude Code

Failure mode

Destructive Action

Root cause

Scope Misunderstanding

Domain

Other

Source

Github Issue