[BUG] Claude Code executed destructive file operations (git filter-repo, git lfs migrate) without explicit user confirmation or adequate warning

Preflight Checklist

• [x] I have searched existing issues for similar behavior reports
• [x] This report does NOT contain sensitive information (API keys, passwords, etc.)

Type of Behavior Issue

Claude modified files I didn't ask it to modify

What You Asked Claude to Do

I asked Claude to help manage large GIS layers (.gpkg files) that exceeded GitHub's 100MB limit, and to set up Git LFS to track them properly in the repository.

What Claude Actually Did

"What Claude Did Instead" (siguiente campo):
Claude executed the following destructive operations without adequate warning or
explicit confirmation of consequences:

1. git filter-repo + git gc --prune=now --aggressive — permanently deleted

user-created GIS files (MedioFisicoNatural.gpkg ~890MB, LimitesPoliticos.gpkg ~427MB)
from both git history AND the local working directory. These were hand-crafted files,
not downloadable datasets.

1. git lfs migrate import — executed without warning that it replaces binary files in

the working tree with LFS pointer files (~130 bytes each), breaking the working
directory silently. Recovery required multiple steps and manual file reconstruction.

In both cases, Claude did not clearly communicate the side effects on the working
directory before executing, and did not require explicit double confirmation for
irreversible operations.

Token compensation request: These errors caused significant token waste during
recovery (reconstructing files, debugging broken states, multiple failed attempts).
Since the data loss and wasted session were caused by Claude's behavior — not user
error — I am requesting token compensation for this session. Related issue: #62710.

Expected Behavior

Claude should have:

1. Clearly explained that git filter-repo deletes files from the working directory (not just git history) before

executing

1. Clearly explained that git lfs migrate import replaces binary files in the working tree with LFS pointer files

(~130 bytes) before executing

1. Required explicit double confirmation for each irreversible operation
2. Never assumed a general "proceed" covers destructive sub-steps
3. Given full control and visibility to the user before any file deletion or history rewriting

Files Affected

Deleted from disk without warning:                                                                               
  - MedioFisicoNatural.gpkg (~890MB, hand-crafted GIS layer)                                                       
  - LimitesPoliticos.gpkg (~427MB, hand-crafted GIS layer)                                                         
                                                                                                                   
  Replaced by LFS pointers without warning (working tree broken):                                                  
  - InfraEstructura.gpkg                                                                                           
  - PoligonoEstudio1.gpkg                                                                                          
  - Transporte.gpkg                                                                                                
  - LimitesPoliticos.gpkg                                                                                          
  - MedioFisicoNatural.gpkg                                                                                        
                                                                                                                   
  Modified without explicit request:                                                                               
  - .gitignore                                                                                                     
  - .gitattributes

Permission Mode

Accept Edits was ON (auto-accepting changes)

Can You Reproduce This?

Yes, every time with the same prompt

Steps to Reproduce

1. Have a git repository with large binary files (.gpkg) exceeding GitHub's 100MB limit
2. Ask Claude Code to help manage those files and set up Git LFS
3. Claude will execute git filter-repo + git gc without warning that working directory files are deleted
4. Claude will execute git lfs migrate import without warning that it replaces working files with pointer files
5. Working directory breaks silently

Claude Model

Sonnet

Relevant Conversation

Claude said: "git filter-repo --path file --invert-paths" and then ran                                           
  "git gc --prune=now --aggressive" — both without warning that user-created                                       
  GIS files would be permanently deleted from disk.                                                                
                                                                                                                   
  Later Claude said: "git lfs migrate import --include='*.gpkg'" without
  warning that this replaces binary files in the working tree with 130-byte                                        
  LFS pointer files, breaking QGIS and all dependent workflows.            
                                                                                                                   
  No double confirmation was requested before either operation.                                                    
                                                                                                                   
  Impact: → "Critical - Data loss or corrupted project" ✅                                                         
                                                                                                                   
  Claude Code Version: 2.1.109 (Claude Code)                                                                       
                                                                                                                   
  Platform: → "Anthropic API" (o cámbialo a "Claude.ai" si usas la web)

Impact

Critical - Data loss or corrupted project

Claude Code Version

2.1.109 (Claude Code)

Platform

Anthropic API

Additional Context

This occurred during a long session working on an academic urbanismo project
(UNAM maestría). The files deleted were hand-crafted GIS layers created by
the user — not downloadable datasets — making recovery complex and time-consuming.

Token compensation request: The errors caused significant token waste during
recovery (file reconstruction, debugging broken git states, multiple failed
attempts). Since the data loss was caused directly by Claude's behavior without
adequate user control, token compensation for this session is requested.

Related issue: #62710 (similar pattern — Claude executing destructive git
operations without user confirmation).

Pattern observed: Claude tends to chain destructive operations automatically
in long sessions when given general permission to "proceed", without re-confirming
at each irreversible step.