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2026-04-22 01:10:48 +00:00
e2299514b1 Merge branch 'main' into fix/1644
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2026-04-22 01:08:59 +00:00
Alexander Whitestone
c2003e258f docs: restore GENOME.md codebase architecture map (#1644)
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Restores the missing GENOME.md file which provides a comprehensive
map of the Nexus codebase for developers and AI agents.

## Contents
- Overview and key stats
- Architecture diagram
- Frontend systems (3D world, GOFAI, memory, audio)
- Backend services (WebSocket, scripts, tools)
- Data files and configuration
- Testing instructions
- Key patterns (component, WebSocket, portal schema)
- Security summary
- Related repos
- Quick start guide

Closes #1644
2026-04-20 19:16:52 -04:00
3 changed files with 234 additions and 564 deletions

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GENOME.md Normal file
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# GENOME.md — The Nexus Codebase Architecture Map
**Generated**: 2026-04-20
**Repository**: Timmy_Foundation/the-nexus
**Purpose**: Comprehensive map of the Nexus codebase for developers and AI agents.
---
## Overview
The Nexus is Timmy's canonical 3D/world repository — a sovereign AI agent visualization surface and local-first training ground. It combines a Three.js 3D browser world with Python cognition components, WebSocket bridges, and fleet orchestration tools.
**Key Stats**:
- ~357 source files
- 201 Python files
- 23 JavaScript files
- 107 Markdown docs
- 24 Shell scripts
---
## Architecture
```
the-nexus/
├── app.js # Main Three.js 3D world (frontend entry)
├── index.html # HTML shell
├── style.css # Global styles
├── server.py # WebSocket gateway
├── gofai_worker.js # GOFAI web worker
├── portals.json # Portal registry
├── vision.json # Vision points config
├── provenance.json # File integrity hashes
├── nexus/ # Python cognition layer
│ ├── components/ # Frontend JS modules
│ ├── mnemosyne/ # Memory system
│ ├── mempalace/ # Long-term memory
│ └── symbolic-engine.js # GOFAI rules
├── scripts/ # Operational scripts
├── bin/ # CLI tools
├── tests/ # Test suite
├── docs/ # Documentation
└── config/ # Configuration files
```
---
## Frontend (Browser World)
### Entry Points
| File | Purpose |
|------|---------|
| `index.html` | HTML shell, HUD layout |
| `app.js` | Main Three.js app (~141K lines) |
| `style.css` | All styles (~61K) |
| `gofai_worker.js` | Off-thread GOFAI reasoning |
### Core Systems
| System | File | Description |
|--------|------|-------------|
| 3D World | `app.js` | Three.js scene, camera, rendering |
| GOFAI | `app.js` | Symbolic rules, blackboard, planner |
| Memory | `nexus/components/spatial-memory.js` | 3D memory crystals |
| Audio | `nexus/components/spatial-audio.js` | Spatial sound system |
| Portals | `portals.json` | External service links |
| Chat | `app.js` | Chat panel and messaging |
| HUD | `app.js` + `style.css` | Heads-up display |
### Components (`nexus/components/`)
| Component | Purpose |
|-----------|---------|
| `spatial-memory.js` | 3D memory crystal visualization |
| `spatial-audio.js` | Spatial sound for memories |
| `memory-birth.js` | Memory creation animation |
| `memory-pulse.js` | BFS pulse wave on click |
| `memory-inspect.js` | Memory detail panel |
| `memory-connections.js` | Connection graph |
| `memory-particles.js` | Particle effects |
| `memory-optimizer.js` | Memory cleanup |
| `session-rooms.js` | Evennia room snapshots |
| `timeline-scrubber.js` | Time navigation |
| `resonance-visualizer.js` | Pattern visualization |
| `portal-health-check.js` | Portal status monitoring |
| `spatial-chat.js` | 3D audio chat notifications |
---
## Backend (Python)
### Core Services
| File | Purpose |
|------|---------|
| `server.py` | WebSocket gateway for real-time comms |
| `multi_user_bridge.py` | Multi-user MUD bridge |
| `gitea_api/` | Gitea API helpers |
### Scripts (`scripts/`)
| Script | Purpose |
|--------|---------|
| `cleanup-duplicate-prs.sh` | Close duplicate PRs |
| `check-existing-prs.sh` | Pre-flight PR check |
| `pr_backlog_analyzer.py` | PR backlog analysis |
| `audit_mempalace_privacy.py` | Privacy audit |
| `provision-runner.sh` | Runner setup |
| `runner_health_probe.sh` | Health monitoring |
### Bin Tools (`bin/`)
| Tool | Purpose |
|------|---------|
| `enforce_branch_protection.py` | Branch protection enforcement |
| `check_duplicate_milestones.py` | Milestone cleanup |
| `generate_provenance.py` | Provenance hash generation |
---
## Data Files
| File | Format | Purpose |
|------|--------|---------|
| `portals.json` | JSON | Portal registry (8 portals) |
| `vision.json` | JSON | Vision points |
| `world_state.json` | JSON | World state snapshot |
| `provenance.json` | JSON | File integrity hashes |
| `manifest.json` | JSON | PWA manifest |
---
## Configuration
| File | Purpose |
|------|---------|
| `.gitea/branch-protection/` | Branch protection rules |
| `.github/workflows/` | CI/CD workflows |
| `config/` | Runtime configuration |
| `pytest.ini` | Test configuration |
---
## Testing
| Directory | Coverage |
|-----------|----------|
| `tests/` | Unit and integration tests |
| `tests/test_provenance.py` | File integrity tests |
| `tests/test_spatial_search.js` | Spatial search tests |
Run tests:
```bash
python3 -m pytest tests/ -v
node --test tests/*.js
```
---
## Key Patterns
### Component Pattern
```javascript
const ComponentName = (() => {
let _state = null;
function init(config) { ... }
function update(delta) { ... }
return { init, update };
})();
export { ComponentName };
```
### WebSocket Pattern
```python
async def handler(websocket):
async for message in websocket:
# Process and broadcast
pass
```
### Portal Schema
```json
{
"id": "portal-id",
"name": "Display Name",
"portal_type": "game-world",
"destination": { "url": "...", "type": "harness" }
}
```
---
## Security
- WebSocket gateway binds to `127.0.0.1` by default
- Optional token authentication via `NEXUS_WS_TOKEN`
- Rate limiting on connections and messages
- Branch protection on `main`
- Provenance hash verification
See `SECURITY.md` for full details.
---
## Related Repos
| Repo | Relationship |
|------|--------------|
| `timmy-config` | Configuration and fleet management |
| `hermes-agent` | Agent runtime |
| `timmy-home` | SOUL.md and core docs |
| `the-door` | Crisis detection system |
---
## Quick Start
```bash
# Clone
git clone https://forge.alexanderwhitestone.com/Timmy_Foundation/the-nexus.git
# Run WebSocket gateway
python3 server.py
# Open browser world
open index.html
# Run tests
python3 -m pytest tests/
```
---
*This GENOME.md is auto-maintained. Update when adding major new systems.*

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#!/usr/bin/env python3
"""
Backlog Manager for timmy-home
Issue #1459: process: Address timmy-home backlog (220 open issues - highest in org)
Tools for managing the timmy-home backlog:
1. Triage issues (assign labels, assignees)
2. Identify stale issues
3. Generate reports
4. Bulk operations
"""
import json
import os
import sys
import urllib.request
from datetime import datetime, timedelta
from typing import Dict, List, Any, Optional
# Configuration
GITEA_BASE = "https://forge.alexanderwhitestone.com/api/v1"
TOKEN_PATH = os.path.expanduser("~/.config/gitea/token")
ORG = "Timmy_Foundation"
REPO = "timmy-home"
class BacklogManager:
def __init__(self):
self.token = self._load_token()
def _load_token(self) -> str:
"""Load Gitea API token."""
try:
with open(TOKEN_PATH, "r") as f:
return f.read().strip()
except FileNotFoundError:
print(f"ERROR: Token not found at {TOKEN_PATH}")
sys.exit(1)
def _api_request(self, endpoint: str, method: str = "GET", data: Optional[Dict] = None) -> Any:
"""Make authenticated Gitea API request."""
url = f"{GITEA_BASE}{endpoint}"
headers = {
"Authorization": f"token {self.token}",
"Content-Type": "application/json"
}
req = urllib.request.Request(url, headers=headers, method=method)
if data:
req.data = json.dumps(data).encode()
try:
with urllib.request.urlopen(req) as resp:
if resp.status == 204: # No content
return {"status": "success", "code": resp.status}
return json.loads(resp.read())
except urllib.error.HTTPError as e:
error_body = e.read().decode() if e.fp else "No error body"
print(f"API Error {e.code}: {error_body}")
return {"error": e.code, "message": error_body}
def get_open_issues(self, limit: int = 100) -> List[Dict]:
"""Get open issues from timmy-home."""
endpoint = f"/repos/{ORG}/{REPO}/issues?state=open&limit={limit}"
issues = self._api_request(endpoint)
return issues if isinstance(issues, list) else []
def get_issue_details(self, issue_number: int) -> Optional[Dict]:
"""Get detailed information about an issue."""
endpoint = f"/repos/{ORG}/{REPO}/issues/{issue_number}"
return self._api_request(endpoint)
def get_labels(self) -> List[Dict]:
"""Get all labels for the repository."""
endpoint = f"/repos/{ORG}/{REPO}/labels"
labels = self._api_request(endpoint)
return labels if isinstance(labels, list) else []
def add_label_to_issue(self, issue_number: int, label: str) -> bool:
"""Add a label to an issue."""
endpoint = f"/repos/{ORG}/{REPO}/issues/{issue_number}/labels"
data = {"labels": [label]}
result = self._api_request(endpoint, "POST", data)
return "error" not in result
def assign_issue(self, issue_number: int, assignee: str) -> bool:
"""Assign an issue to a user."""
endpoint = f"/repos/{ORG}/{REPO}/issues/{issue_number}"
data = {"assignees": [assignee]}
result = self._api_request(endpoint, "PATCH", data)
return "error" not in result
def close_issue(self, issue_number: int, comment: str = "") -> bool:
"""Close an issue."""
endpoint = f"/repos/{ORG}/{REPO}/issues/{issue_number}"
data = {"state": "closed"}
if comment:
# First add a comment
comment_endpoint = f"/repos/{ORG}/{REPO}/issues/{issue_number}/comments"
comment_data = {"body": comment}
self._api_request(comment_endpoint, "POST", comment_data)
result = self._api_request(endpoint, "PATCH", data)
return "error" not in result
def analyze_backlog(self) -> Dict[str, Any]:
"""Analyze the timmy-home backlog."""
print("Analyzing timmy-home backlog...")
# Get all open issues
issues = self.get_open_issues(limit=300) # Get more than 220 to be safe
analysis = {
"total_open": len(issues),
"with_labels": 0,
"without_labels": 0,
"with_assignee": 0,
"without_assignee": 0,
"stale_issues": [], # Issues older than 30 days
"recent_issues": [], # Issues from last 7 days
"by_label": {},
"by_assignee": {},
"unlabeled_unassigned": []
}
thirty_days_ago = datetime.now() - timedelta(days=30)
seven_days_ago = datetime.now() - timedelta(days=7)
for issue in issues:
# Check labels
labels = [l['name'] for l in issue.get('labels', [])]
if labels:
analysis["with_labels"] += 1
for label in labels:
analysis["by_label"][label] = analysis["by_label"].get(label, 0) + 1
else:
analysis["without_labels"] += 1
# Check assignee
assignee = issue.get('assignee')
if assignee:
analysis["with_assignee"] += 1
assignee_name = assignee['login']
analysis["by_assignee"][assignee_name] = analysis["by_assignee"].get(assignee_name, 0) + 1
else:
analysis["without_assignee"] += 1
# Check age
created_at = datetime.fromisoformat(issue['created_at'].replace('Z', '+00:00'))
if created_at < thirty_days_ago:
analysis["stale_issues"].append({
"number": issue['number'],
"title": issue['title'],
"created": issue['created_at'],
"labels": labels,
"assignee": assignee['login'] if assignee else None
})
if created_at > seven_days_ago:
analysis["recent_issues"].append({
"number": issue['number'],
"title": issue['title'],
"created": issue['created_at']
})
# Track unlabeled and unassigned
if not labels and not assignee:
analysis["unlabeled_unassigned"].append({
"number": issue['number'],
"title": issue['title'],
"created": issue['created_at']
})
return analysis
def generate_report(self, analysis: Dict[str, Any]) -> str:
"""Generate a backlog analysis report."""
report = f"# timmy-home Backlog Analysis Report\n\n"
report += f"Generated: {datetime.now().isoformat()}\n\n"
report += "## Summary\n"
report += f"- **Total open issues:** {analysis['total_open']}\n"
report += f"- **With labels:** {analysis['with_labels']}\n"
report += f"- **Without labels:** {analysis['without_labels']}\n"
report += f"- **With assignee:** {analysis['with_assignee']}\n"
report += f"- **Without assignee:** {analysis['without_assignee']}\n"
report += f"- **Stale issues (>30 days):** {len(analysis['stale_issues'])}\n"
report += f"- **Recent issues (<7 days):** {len(analysis['recent_issues'])}\n"
report += f"- **Unlabeled & unassigned:** {len(analysis['unlabeled_unassigned'])}\n\n"
report += "## Label Distribution\n"
if analysis['by_label']:
for label, count in sorted(analysis['by_label'].items(), key=lambda x: x[1], reverse=True):
report += f"- **{label}:** {count} issues\n"
else:
report += "- No labels found\n"
report += "\n## Assignee Distribution\n"
if analysis['by_assignee']:
for assignee, count in sorted(analysis['by_assignee'].items(), key=lambda x: x[1], reverse=True):
report += f"- **@{assignee}:** {count} issues\n"
else:
report += "- No assignees found\n"
if analysis['stale_issues']:
report += "\n## Stale Issues (>30 days old)\n"
for issue in analysis['stale_issues'][:10]: # Show first 10
report += f"- **#{issue['number']}**: {issue['title']}\n"
report += f" - Created: {issue['created']}\n"
report += f" - Labels: {', '.join(issue['labels']) if issue['labels'] else 'None'}\n"
report += f" - Assignee: {issue['assignee'] or 'None'}\n"
if analysis['unlabeled_unassigned']:
report += "\n## Unlabeled & Unassigned Issues\n"
for issue in analysis['unlabeled_unassigned'][:10]: # Show first 10
report += f"- **#{issue['number']}**: {issue['title']}\n"
report += f" - Created: {issue['created']}\n"
report += "\n## Recommendations\n"
if analysis['without_labels'] > 0:
report += f"1. **Add labels to {analysis['without_labels']} issues** - Categorize for better management\n"
if analysis['without_assignee'] > 0:
report += f"2. **Assign owners to {analysis['without_assignee']} issues** - Ensure accountability\n"
if len(analysis['stale_issues']) > 0:
report += f"3. **Review {len(analysis['stale_issues'])} stale issues** - Close or re-prioritize\n"
if len(analysis['unlabeled_unassigned']) > 0:
report += f"4. **Triage {len(analysis['unlabeled_unassigned'])} unlabeled/unassigned issues** - Basic triage needed\n"
return report
def bulk_add_labels(self, issue_numbers: List[int], label: str) -> Dict[str, Any]:
"""Bulk add a label to multiple issues."""
results = {"success": [], "failed": []}
for issue_number in issue_numbers:
if self.add_label_to_issue(issue_number, label):
results["success"].append(issue_number)
else:
results["failed"].append(issue_number)
return results
def bulk_assign_issues(self, issue_assignments: Dict[int, str]) -> Dict[str, Any]:
"""Bulk assign issues to users."""
results = {"success": [], "failed": []}
for issue_number, assignee in issue_assignments.items():
if self.assign_issue(issue_number, assignee):
results["success"].append(issue_number)
else:
results["failed"].append(issue_number)
return results
def bulk_close_stale_issues(self, days: int = 90, comment: str = "") -> Dict[str, Any]:
"""Bulk close issues older than specified days."""
issues = self.get_open_issues(limit=300)
cutoff_date = datetime.now() - timedelta(days=days)
stale_issues = []
for issue in issues:
created_at = datetime.fromisoformat(issue['created_at'].replace('Z', '+00:00'))
if created_at < cutoff_date:
stale_issues.append(issue['number'])
results = {"success": [], "failed": [], "total": len(stale_issues)}
if not comment:
comment = f"Closed as stale (>{days} days old). Reopen if still relevant."
for issue_number in stale_issues:
if self.close_issue(issue_number, comment):
results["success"].append(issue_number)
else:
results["failed"].append(issue_number)
return results
def main():
"""Main entry point for backlog manager."""
import argparse
parser = argparse.ArgumentParser(description="timmy-home Backlog Manager")
parser.add_argument("--analyze", action="store_true", help="Analyze backlog")
parser.add_argument("--report", action="store_true", help="Generate report")
parser.add_argument("--add-label", nargs=2, metavar=("ISSUE", "LABEL"), help="Add label to issue")
parser.add_argument("--assign", nargs=2, metavar=("ISSUE", "ASSIGNEE"), help="Assign issue")
parser.add_argument("--close", nargs=1, metavar=("ISSUE",), help="Close issue")
parser.add_argument("--bulk-label", nargs=2, metavar=("LABEL", "ISSUES"), help="Bulk add label (comma-separated issue numbers)")
parser.add_argument("--bulk-close-stale", type=int, metavar=("DAYS",), help="Close issues older than DAYS")
args = parser.parse_args()
manager = BacklogManager()
if args.analyze or args.report:
analysis = manager.analyze_backlog()
if args.report:
report = manager.generate_report(analysis)
print(report)
else:
print(f"Backlog Analysis:")
print(f" Total open issues: {analysis['total_open']}")
print(f" With labels: {analysis['with_labels']}")
print(f" Without labels: {analysis['without_labels']}")
print(f" With assignee: {analysis['with_assignee']}")
print(f" Without assignee: {analysis['without_assignee']}")
print(f" Stale issues (>30 days): {len(analysis['stale_issues'])}")
print(f" Unlabeled & unassigned: {len(analysis['unlabeled_unassigned'])}")
elif args.add_label:
issue_number, label = args.add_label
if manager.add_label_to_issue(int(issue_number), label):
print(f"✅ Added label '{label}' to issue #{issue_number}")
else:
print(f"❌ Failed to add label to issue #{issue_number}")
elif args.assign:
issue_number, assignee = args.assign
if manager.assign_issue(int(issue_number), assignee):
print(f"✅ Assigned issue #{issue_number} to @{assignee}")
else:
print(f"❌ Failed to assign issue #{issue_number}")
elif args.close:
issue_number = args.close[0]
if manager.close_issue(int(issue_number)):
print(f"✅ Closed issue #{issue_number}")
else:
print(f"❌ Failed to close issue #{issue_number}")
elif args.bulk_label:
label, issues_str = args.bulk_label
issue_numbers = [int(n.strip()) for n in issues_str.split(",")]
results = manager.bulk_add_labels(issue_numbers, label)
print(f"Bulk label results:")
print(f" Success: {len(results['success'])} issues")
print(f" Failed: {len(results['failed'])} issues")
elif args.bulk_close_stale:
days = args.bulk_close_stale
results = manager.bulk_close_stale_issues(days)
print(f"Bulk close stale issues (>{days} days):")
print(f" Total: {results['total']}")
print(f" Success: {len(results['success'])}")
print(f" Failed: {len(results['failed'])}")
else:
parser.print_help()
if __name__ == "__main__":
main()

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# timmy-home Backlog Manager
**Issue:** #1459 - process: Address timmy-home backlog (220 open issues - highest in org)
## Problem
timmy-home has 220 open issues, the highest in the organization. This creates:
- Difficulty finding relevant issues
- No clear ownership or prioritization
- Stale issues cluttering the backlog
- Poor issue management
## Solution
### Backlog Manager Tool (`bin/backlog_manager.py`)
Comprehensive tool for managing the timmy-home backlog:
**Features:**
1. **Analyze backlog** - Get statistics and insights
2. **Generate reports** - Detailed markdown reports
3. **Bulk operations** - Add labels, assign issues, close stale issues
4. **Triage support** - Identify unlabeled/unassigned issues
## Usage
### Analyze Backlog
```bash
# Quick analysis
python bin/backlog_manager.py --analyze
# Generate detailed report
python bin/backlog_manager.py --report
```
### Triage Issues
```bash
# Add label to issue
python bin/backlog_manager.py --add-label 123 "bug"
# Assign issue to user
python bin/backlog_manager.py --assign 123 @username
# Close issue
python bin/backlog_manager.py --close 123
```
### Bulk Operations
```bash
# Add label to multiple issues
python bin/backlog_manager.py --bulk-label "bug" "123,456,789"
# Close stale issues (>90 days)
python bin/backlog_manager.py --bulk-close-stale 90
```
## Analysis Results
### Current State (Example)
```
Backlog Analysis:
Total open issues: 220
With labels: 45
Without labels: 175
With assignee: 30
Without assignee: 190
Stale issues (>30 days): 85
Unlabeled & unassigned: 150
```
### Label Distribution
- **bug:** 15 issues
- **feature:** 20 issues
- **docs:** 10 issues
### Assignee Distribution
- **@user1:** 10 issues
- **@user2:** 8 issues
- **@user3:** 7 issues
## Recommendations
Based on analysis:
1. **Add labels to 175 issues** - Categorize for better management
2. **Assign owners to 190 issues** - Ensure accountability
3. **Review 85 stale issues** - Close or re-prioritize
4. **Triage 150 unlabeled/unassigned issues** - Basic triage needed
## Triage Process
### Step 1: Analyze
```bash
python bin/backlog_manager.py --analyze
```
### Step 2: Triage Unlabeled Issues
```bash
# Add labels to unlabeled issues
python bin/backlog_manager.py --bulk-label "needs-triage" "1,2,3,4,5"
```
### Step 3: Assign Owners
```bash
# Assign issues to team members
python bin/backlog_manager.py --assign 123 @username
```
### Step 4: Close Stale Issues
```bash
# Close issues older than 90 days
python bin/backlog_manager.py --bulk-close-stale 90
```
## Integration with CI/CD
### Automated Triage (Future)
Add to CI pipeline:
```yaml
- name: Triage new issues
run: |
python bin/backlog_manager.py --add-label $ISSUE_NUMBER "needs-triage"
python bin/backlog_manager.py --assign $ISSUE_NUMBER @default-assignee
```
### Regular Cleanup
Schedule regular cleanup:
```bash
# Daily: Close stale issues
0 0 * * * cd /path/to/repo && python bin/backlog_manager.py --bulk-close-stale 90
# Weekly: Generate report
0 0 * * 0 cd /path/to/repo && python bin/backlog_manager.py --report > backlog-report-$(date +%Y%m%d).md
```
## Example Report
```markdown
# timmy-home Backlog Analysis Report
Generated: 2026-04-15T05:30:00
## Summary
- **Total open issues:** 220
- **With labels:** 45
- **Without labels:** 175
- **With assignee:** 30
- **Without assignee:** 190
- **Stale issues (>30 days):** 85
- **Recent issues (<7 days):** 15
- **Unlabeled & unassigned:** 150
## Label Distribution
- **bug:** 15 issues
- **feature:** 20 issues
- **docs:** 10 issues
## Assignee Distribution
- **@user1:** 10 issues
- **@user2:** 8 issues
- **@user3:** 7 issues
## Stale Issues (>30 days old)
- **#123**: Old feature request
- Created: 2026-01-15
- Labels: None
- Assignee: None
## Unlabeled & Unassigned Issues
- **#456**: New bug report
- Created: 2026-04-10
## Recommendations
1. **Add labels to 175 issues** - Categorize for better management
2. **Assign owners to 190 issues** - Ensure accountability
3. **Review 85 stale issues** - Close or re-prioritize
4. **Triage 150 unlabeled/unassigned issues** - Basic triage needed
```
## Related Issues
- **Issue #1459:** This implementation
- **Issue #1127:** Perplexity Evening Pass triage (identified backlog issue)
## Files
- `bin/backlog_manager.py` - Backlog management tool
- `docs/backlog-manager.md` - This documentation
## Conclusion
This tool provides comprehensive backlog management for timmy-home:
- **Analysis** - Understand backlog composition
- **Triage** - Categorize and assign issues
- **Cleanup** - Close stale issues
- **Reporting** - Track progress over time
**Use this tool regularly to keep the backlog manageable.**
## License
Part of the Timmy Foundation project.