Agent Creates New Files Instead of Editing Existing Ones — Duplicate File Proliferation

Symptom

Directory fills with *_new.py, *_v2.py, *_updated.yaml files
Agent creates auth_fixed.py when auth.py should have been edited
Agent writes a complete replacement file instead of making surgical edits
Import references still point to old file — new file is never used
After 10 sessions, there are multiple versions of the same module

Root Cause

Without explicit instruction to edit existing files, the model defaults to “create a new version” — a safe approach that avoids risking the original. This is especially common when the agent is uncertain about modifying existing code or when it was trained on examples that create new files.

Fix

Option 1: Explicit “edit existing” instruction

System prompt:
"File management rules:
- ALWAYS edit existing files rather than creating new ones
- NEVER create files named *_new.*, *_v2.*, *_updated.*, *_fixed.*, *_backup.*
- If a file exists: open it, find the section to change, edit in place
- Only create a new file if it genuinely doesn't exist yet

Bad: 'I'll create auth_fixed.py with the corrected code'
Good: 'I'll edit line 47 of auth.py to fix the null check'"

Option 2: Read-before-write requirement

System prompt:
"Before writing any file:
1. Check if a file with that name or purpose already exists
2. If yes: edit the existing file — do not create a new one
3. If no: then create it

Never write a file without first searching for existing files with similar names."

Option 3: Surgical edit instruction

System prompt:
"When fixing code, make the minimum change necessary:
- Find the specific function/line that needs changing
- Edit only that part
- Leave all other code unchanged

Do not rewrite entire files. Do not create replacement versions.
Show the diff of what changed, not the complete new file."

Option 4: Detect and prevent duplicate creation

import os, glob

def prevent_duplicate_file(proposed_path, agent_response):
    """Check if agent is about to create a duplicate"""
    DUPLICATE_PATTERNS = ['_new.', '_v2.', '_updated.', '_fixed.', '_backup.', '_copy.']

    filename = os.path.basename(proposed_path)
    if any(p in filename for p in DUPLICATE_PATTERNS):
        # Find the likely original
        base = re.sub(r'_(new|v2|updated|fixed|backup|copy)', '', os.path.splitext(filename)[0])
        originals = glob.glob(f"**/{base}.*", recursive=True)
        if originals:
            return f"Warning: {proposed_path} looks like a duplicate of {originals}. Edit the original instead."
    return None

Option 5: Git-based verification

# After agent session — check for new files that shouldn't exist
git status | grep "??"  # Untracked files

# Check for suspicious naming patterns
git status | grep -E "_(new|v2|updated|fixed|backup)\."

# If found — check if they should have been edits instead
git diff HEAD -- the_original_file.py

Cleanup Strategy

import os, glob, re

def find_agent_duplicates(directory="."):
    """Find files that look like agent-created duplicates"""
    pattern = re.compile(r'_(new|v2|updated|fixed|backup|copy|2)\.(py|js|ts|yaml|json|md)$')
    duplicates = []

    for path in glob.glob(f"{directory}/**/*", recursive=True):
        if pattern.search(os.path.basename(path)):
            # Check if original exists
            original = pattern.sub(r'.\2', os.path.basename(path))  # Simplified
            duplicates.append({"duplicate": path, "possible_original": original})

    return duplicates

Expected Token Savings

Cleaning up duplicate file proliferation after 10 sessions: ~8,000 tokens Explicit edit-existing instruction: prevents all duplicates

Environment

Any code-editing agent with file creation capability
Source: direct experience, very common in agent-assisted development

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