Mysterious Empty File Creation - Forensic Investigation

[triadflow]

🚨 Critical Issue: Repeated Empty File Creation

Problem Summary

Empty files are being automatically created in our repository multiple times despite manual deletion. This is not a memory issue (happening in small workspace) and requires forensic investigation to identify the root cause.

🔍 Forensic Evidence

Pattern Identified

• Files affected: copilot_context_theory.md, test.py, workspace_analyzer_enhanced.py, compare_folders.py, and others
• Behavior: Files are created as empty (0 bytes)
• Frequency: Recreated automatically after manual deletion
• Timing: All files created at identical timestamps (suspicious automated process)

Key Observations

1. This is the 2nd time this has happened - there's a repeating pattern
2. Small workspace context - not related to memory pressure from large repositories
3. Identical timestamps suggest automated process, not user action
4. VS Code Helper processes have these files open (confirmed via lsof)

📦 Forensic Evidence Package

The following log files and evidence have been collected:

File System Forensics

• file_forensics.txt - Detailed stat output for all affected files
• all_empty_files.txt - Complete list of empty files in project
• open_files.txt - Processes that have problematic files open

Process Analysis

• running_processes.txt - All VS Code/Copilot related processes
• system_logs.txt - System logs from last 2 hours

Git Context

• git_status.txt - Current repository state
• recent_git_history.txt - Recent commits for context

Environment Info

• investigation_metadata.txt - Timestamps and VS Code version

🕵️ Investigation Questions

Primary Suspects

1. GitHub Copilot Extension - Creating placeholder files for suggestions?
2. VS Code Language Servers - TypeScript/Python servers creating temp files?
3. VS Code Auto-save/Recovery - Attempting to restore deleted files?
4. Extension Conflict - Multiple extensions trying to create the same files?
5. VS Code Workspace Sync - Syncing with cloud/settings causing recreation?

Key Questions to Answer

• What process is creating these files at identical timestamps?
• Why are they created empty instead of with content?
• What triggers the recreation after deletion?
• Is this related to VS Code's file watching system?
• Are extensions trying to "restore" files they think should exist?

🔬 Analysis Needed

Immediate Investigation Steps

1. Analyze the forensic logs to identify the exact process creating files
2. Check VS Code extension logs for file creation activities
3. Monitor file system events during file recreation
4. Test with VS Code extensions disabled to isolate the cause
5. Check VS Code workspace settings for auto-recovery features

System Context

• OS: macOS
• Environment: Development workspace with GitHub Copilot
• Repository: Small project (~40 files), not memory-constrained
• Previous occurrence: This is the second time this pattern has occurred

🎯 Expected Outcome

Success Criteria

• Identify the exact process/extension creating empty files
• Understand why files are created empty vs with content
• Implement a proper fix that stops the root cause
• Document prevention strategy for future occurrences

Not Acceptable Solutions

• ❌ Adding files to .gitignore (hides symptom, doesn't solve cause)
• ❌ Assuming it's a memory issue (evidence shows otherwise)
• ❌ Manual deletion without addressing root cause

🚀 Priority: HIGH

This issue indicates a fundamental problem with our development environment that will continue to cause confusion and git repository pollution until resolved.

📋 Evidence Files Attached

All forensic evidence is collected in the empty_files_investigation/ directory and ready for analysis.

🔍 Current Forensic Data Analysis

Existing Evidence Analysis Required

We currently have empty files that were created at identical timestamps (Jun 22 09:24:33 2025) - this is our smoking gun evidence that needs analysis FIRST before any restoration attempt.

Current Evidence Package Analysis

The empty_files_investigation/ directory contains:

• file_forensics.txt - All files created at EXACT same second (automated process confirmed)
• running_processes.txt - Multiple VS Code Helper processes active
• open_files.txt - Which processes have empty files open
• system_logs.txt - System activity during file creation period

Key Finding from Current Data

All files show creation time: "Jun 22 09:24:33 2025" - this timestamp precision indicates:

• ✅ Automated batch process (not manual/user action)
• ✅ Single trigger event that created all files simultaneously
• ✅ VS Code Helper processes identified in forensics
• ✅ Repeating pattern (2nd occurrence documented)

🧪 Proposed Restoration Test Strategy

Critical Understanding: The Restoration Trigger

When we restore Git state (remove empty files), we expect the SAME PROCESS that originally created them will detect the "missing" files and recreate them immediately. This is our opportunity to catch the culprit in real-time.

Phase 1: Analyze Current Evidence (NOW)

Before restoration, we must analyze existing forensic data to form hypotheses about what process is responsible.

Phase 2: Deploy Monitoring (BEFORE Restoration)

Set up comprehensive monitoring to capture the recreation event when it happens.

Phase 3: Trigger Recreation (Git Restoration)

Restore Git state while monitoring is active - this should trigger immediate file recreation.

Phase 4: Capture and Analyze

Identify the exact process, timing, and mechanism of file recreation.

�️ Monitoring Tooling Created

Note: Tooling Already Developed

During this investigation, comprehensive monitoring scripts have been created in /github_issue/monitoring_scripts/. While the GitHub issue was intended to propose tooling, the urgency of the investigation led to immediate development.

Available Monitoring Arsenal

The following monitoring tools are ready for deployment during Git restoration:

• master_monitor.sh - Orchestrates all monitoring scripts
• file_creation_monitor.sh - Real-time file system event capture
• process_activity_monitor.sh - VS Code process tracking and memory monitoring
• extension_activity_tracker.sh - Extension behavior and log analysis
• git_state_capture.sh - Complete Git state snapshots (before/after)
• stop_monitoring.sh - Clean shutdown and evidence packaging

Deployment Strategy for Git Restoration

Script 1: Real-Time File System Monitor

#!/bin/bash
# file_creation_monitor.sh - Monitor file creation in real-time
echo "🔍 Starting file system monitor for empty file creation..."
echo "Monitoring: /Users/reneluijk/projects/test_mem_vcode"
echo "Timestamp: $(date)"

# Monitor file creation events
fswatch -0 /Users/reneluijk/projects/test_mem_vcode | while read -d "" event; do
    if [[ "$event" =~ \.(md|py)$ ]]; then
        echo "[$(date)] FILE EVENT: $event"
        # Check if file is empty
        if [ -f "$event" ] && [ ! -s "$event" ]; then
            echo "🚨 EMPTY FILE CREATED: $event"
            echo "Process list at time of creation:"
            ps aux | grep -E "(code|copilot|vscode)" | head -5
            echo "Files open by VS Code:"
            lsof | grep "$event" || echo "No processes have file open yet"
            echo "---"
        fi
    fi
done

Script 2: Process Activity Logger

#!/bin/bash
# process_activity_monitor.sh - Log VS Code process activities
echo "📊 Starting VS Code process activity monitor..."
echo "Timestamp: $(date)"

while true; do
    # Log VS Code processes every 30 seconds
    echo "[$(date)] VS Code Processes:" >> vscode_process_log.txt
    ps aux | grep -E "(code|copilot)" | grep -v grep >> vscode_process_log.txt
    echo "---" >> vscode_process_log.txt
    
    # Check for new empty files every 10 seconds
    find /Users/reneluijk/projects/test_mem_vcode -name "*.md" -o -name "*.py" | xargs wc -l | grep " 0 " > current_empty_files.txt
    if ! cmp -s current_empty_files.txt last_empty_files.txt 2>/dev/null; then
        echo "🚨 [$(date)] NEW EMPTY FILES DETECTED!" >> vscode_process_log.txt
        diff last_empty_files.txt current_empty_files.txt >> vscode_process_log.txt || true
        cp current_empty_files.txt last_empty_files.txt
    fi
    
    sleep 10
done

Script 3: VS Code Extension Activity Tracker

#!/bin/bash
# extension_activity_tracker.sh - Monitor VS Code extension logs
echo "🔌 Starting VS Code extension activity tracker..."

# Monitor VS Code logs
tail -f ~/Library/Application\ Support/Code/logs/*/main.log 2>/dev/null | while read line; do
    if [[ "$line" =~ (copilot|file|create|write|workspace) ]]; then
        echo "[$(date)] VS Code Log: $line"
    fi
done &

# Monitor Console logs for VS Code
log stream --predicate 'processImagePath contains "Code"' --info | while read line; do
    if [[ "$line" =~ (file|create|write|workspace) ]]; then
        echo "[$(date)] System Log: $line"
    fi
done

Script 4: Git State Capture Script

#!/bin/bash
# git_state_capture.sh - Capture complete git state before/after
echo "📸 Capturing Git state..."

capture_git_state() {
    local suffix=$1
    echo "=== Git State Capture $suffix ===" > git_state_$suffix.txt
    echo "Timestamp: $(date)" >> git_state_$suffix.txt
    echo "Git Status:" >> git_state_$suffix.txt
    git status --porcelain >> git_state_$suffix.txt
    echo "Git Log (last 5):" >> git_state_$suffix.txt
    git log --oneline -5 >> git_state_$suffix.txt
    echo "File timestamps:" >> git_state_$suffix.txt
    find . -name "*.md" -o -name "*.py" | head -20 | xargs stat >> git_state_$suffix.txt
}

capture_git_state "before_deletion"
echo "Git state captured. Run this script again with 'after' to capture post-deletion state."

🎯 Git Restoration Test Protocol

The Critical Moment: Git Restoration

When we restore the Git state to remove empty files, we anticipate the process that originally created them will immediately detect their absence and recreate them. This recreation event is what we need to capture.

Pre-Restoration Analysis Required

Before triggering restoration, analyze current forensic evidence to form hypotheses:

1. Which VS Code Helper process is most likely responsible?
2. What VS Code extension might be tracking these files?
3. What timestamps/patterns can help us correlate the recreation?

Restoration Trigger Protocol

Step 1: Analyze Current Evidence

# Examine existing forensic data
cat empty_files_investigation/file_forensics.txt
head -20 empty_files_investigation/running_processes.txt

Step 2: Deploy Monitoring (Before Restoration)

# Start all monitoring scripts in background
cd github_issue/monitoring_scripts
./master_monitor.sh

Step 3: Git Restoration Trigger (While Monitoring)

# This is the moment we expect immediate recreation
git checkout HEAD -- copilot_context_theory.md copilot_deep_theory.md test.py workspace_analyzer_enhanced.py compare_folders.py
# OR alternative restoration method:
git clean -f *.md *.py  # Remove untracked empty files

Step 4: Capture Recreation Event

• Monitor scripts will capture the immediate recreation
• Expected timeframe: Seconds to minutes after restoration
• Stop monitoring once recreation is confirmed

Step 5: Analysis

# Collect all monitoring data
./stop_monitoring.sh
# This packages all evidence for final analysis

🔬 Advanced Debugging Scenarios

Scenario A: Extension-Specific Testing

# Test with minimal extensions
code --disable-extensions /path/to/workspace
# Then enable extensions one by one to isolate culprit

Scenario B: File Watching Analysis

# Check VS Code file watchers
lsof | grep -E "(inotify|fsevents)" | grep -E "(code|vscode)"

Scenario C: Workspace Settings Investigation

# Backup and test with minimal workspace settings
cp .vscode/settings.json .vscode/settings.json.backup
echo '{}' > .vscode/settings.json

📊 Data Collection Targets

Primary Evidence Needed

1. Exact process ID that creates the files
2. Extension name (if extension-caused)
3. VS Code feature (auto-save, recovery, etc.)
4. Trigger event (what causes the recreation)
5. Timing pattern (immediate, delayed, periodic)

Secondary Evidence

1. File system events leading up to creation
2. Network activity (if cloud sync related)
3. Memory usage patterns during recreation
4. VS Code logs with relevant timestamps

🚀 Execution Plan

When to Execute Restoration Test

• After analyzing current forensic evidence to form hypotheses
• With full monitoring active to capture recreation event
• During active development session when VS Code processes are running
• When we can dedicate time to immediate analysis of results

Expected Recreation Timeline

Based on the identical timestamps in current evidence, we expect:

• Immediate recreation (within seconds of restoration)
• Batch recreation (all files created simultaneously)
• Same timestamp pattern as previous occurrences

Success Criteria

• ✅ Identify exact process creating files
• ✅ Understand why files are empty vs populated
• ✅ Determine root cause (extension, VS Code bug, settings)
• ✅ Implement permanent fix

Deliverables

1. Complete reproduction evidence with process identification
2. Root cause analysis with specific culprit identified
3. Permanent solution implemented and tested
4. Prevention strategy to avoid future occurrences

🛡️ Backup & Safety

Before Testing

# Create safety backup
git stash push -m "Before empty file investigation"
git branch backup-before-investigation

Rollback Plan

# If testing breaks anything
git stash pop
git checkout backup-before-investigation

🚀 READY FOR RESTORATION TEST

Current Status: Evidence Collected, Tooling Ready

We have:

• ✅ Existing forensic evidence from current empty files (identical timestamps)
• ✅ Complete monitoring arsenal created and ready for deployment
• ✅ Restoration trigger plan to provoke recreation event
• ✅ Automated evidence collection system prepared

Next Action: Analyze Then Test

# STEP 1: Analyze current evidence first
cat empty_files_investigation/file_forensics.txt | grep "Jun 22 09:24:33"

# STEP 2: Deploy monitoring before restoration
cd github_issue/monitoring_scripts
./master_monitor.sh

# STEP 3: Trigger recreation via Git restoration
git checkout HEAD -- copilot_context_theory.md test.py workspace_analyzer_enhanced.py compare_folders.py copilot_deep_theory.md

# STEP 4: Capture recreation and analyze
./stop_monitoring.sh

Expected Result

This restoration test will definitively identify:

• Exact process that monitors for "missing" files and recreates them
• Trigger mechanism that detects file absence
• Recreation timing and batch behavior
• Root cause (extension, VS Code feature, or system process)

The key insight: The process that created files originally is likely monitoring for their presence and will recreate them immediately when they're removed via Git restoration.

README.md

monitoring_scripts_package.zip

empty_files_forensic_evidence.zip