fix(audit): resolve 6 critical bugs + standardize project files

.dockerignore

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+# Git
+.git
+.gitignore
+.gitattributes
+
+# Secrets
+.env
+.env.*
+.secrets/
+certs/
+*.pem
+*.key
+
+# Models
+models/
+*.gguf
+
+# Data
+data/
+knowledge-base/
+email-queue/
+
+# IDE
+.idea/
+.vscode/
+*.swp
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Logs
+*.log
+
+# CI
+.github/
+
+# Docker
+Dockerfile*
+docker-compose*
+
+# Node (for tools-ui)
+node_modules/
+
+# Documentation
+README.md
+CONTRIBUTING.md
+SECURITY.md
+CODE_OF_CONDUCT.md
+AUDIT_REPORT.md

.github/CODEOWNERS

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+# Default owners for all files
+* @OneByJorah
+
+# Security-sensitive files
+SECURITY.md @OneByJorah
+config/ @OneByJorah
+docker-compose*.yml @OneByJorah
+Dockerfile* @OneByJorah
+
+# CI/CD
+.github/workflows/ @OneByJorah
+.github/dependabot.yml @OneByJorah

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug Report
+about: Create a report to help us improve
+title: '[BUG] '
+labels: bug
+assignees: ''
+
+---
+
+**Describe the Bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected Behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Environment (please complete the following information):**
+- OS: [e.g. Ubuntu 22.04]
+- Python Version: [e.g. 3.11]
+- Docker Version: [e.g. 24.0]
+
+**Additional Context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature Request
+about: Suggest an idea for this project
+title: '[FEATURE] '
+labels: enhancement
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the Solution You'd Like**
+A clear and concise description of what you want to happen.
+
+**Describe Alternatives You've Considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional Context**
+Add any other context or screenshots about the feature request here.

.github/PULL_REQUEST_TEMPLATE.md

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+## Description
+
+Please include a summary of the change and which issue is fixed.
+
+Fixes # (issue)
+
+## Type of Change
+
+- [ ] Bug fix (non-breaking change)
+- [ ] New feature (non-breaking change)
+- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
+- [ ] Documentation update
+- [ ] Security fix
+
+## Checklist
+
+- [ ] My code follows the style guidelines of this project
+- [ ] I have performed a self-review of my own code
+- [ ] I have commented my code, particularly in hard-to-understand areas
+- [ ] I have made corresponding changes to the documentation
+- [ ] My changes generate no new warnings
+- [ ] I have added tests that prove my fix is effective or that my feature works
+- [ ] New and existing unit tests pass locally with my changes

.github/dependabot.yml

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+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    open-pull-requests-limit: 10
+  - package-ecosystem: "npm"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    open-pull-requests-limit: 10
+  - package-ecosystem: "docker"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    open-pull-requests-limit: 5
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/codeql.yml

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+name: CodeQL
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  schedule:
+    - cron: '0 0 * * 0'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: ['python', 'javascript', 'typescript']
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v3
+        with:
+          languages: ${{ matrix.language }}
+
+      - name: Autobuild
+        uses: github/codeql-action/autobuild@v3
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v3

AUDIT_REPORT.md

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+# AUDIT_REPORT — CommandDesk
+
+**Date:** 2026-07-05
+**Auditor:** J1-PIPELINE (Phase 1 — AUDITOR)
+**Status:** `DEGRADED` (Score: 74/100)
+
+---
+
+## 1. PROJECT CLASSIFICATION
+
+| Field | Value |
+|---|---|
+| **Repo** | CommandDesk |
+| **Class** | AI / Helpdesk / Full-Stack |
+| **Primary Language** | Python 3.11 |
+| **Framework** | FastAPI |
+| **Deployment** | Docker Compose |
+| **Tailscale Only** | No (exposed ports: 80, 443, 8383) |
+
+---
+
+## 2. README COMPLIANCE (README_STANDARD.md)
+
+| Requirement | Status | Notes |
+|---|---|---|
+| One-line positioning | ✅ | "Self-Hosted AI Helpdesk Agent" |
+| Max 3 badges | ❌ | Has **5 badges** (Python, FastAPI, Docker, AI, MIT) |
+| 60-second quick start | ✅ | `git clone` → `cp .env.example .env` → `docker compose up -d` |
+| Features (3-5 bullets) | ✅ | 8 features listed |
+| Architecture diagram | ✅ | ASCII diagram present |
+| Contributing section | ✅ | Links to CONTRIBUTING.md |
+| License section | ✅ | MIT |
+
+**Issue:** README has 5 badges — exceeds the 3-badge max per README_STANDARD.md.
+
+---
+
+## 3. CODE QUALITY — CRITICAL & DEGRADED ITEMS
+
+### 🔴 CRITICAL (Must Fix)
+
+| # | File | Issue | Severity |
+|---|---|---|---|
+| C1 | `rate_limiter.py:64` | **Bug:** `self._sessions: dict[str, SessionState] =()` — Empty tuple instead of dict `{}`. Causes `AttributeError` on first access. | CRITICAL |
+| C2 | `zammad.py` | **Missing import:** Uses `requests.post()`, `requests.patch()`, `requests.get()` but `import requests` is missing. Will crash at runtime. | CRITICAL |
+| C3 | `session_manager.py:38` | **SQL Injection:** `INTERVAL '{} seconds'".format(self.max_duration)` — Uses string formatting for SQL query parameter. | CRITICAL |
+| C4 | `health_monitor.py:22` | **Wrong Redis URL:** `redis://redis:***@postgres:5432/helpdesk` — References PostgreSQL port (5432) instead of Redis port (6379), and uses `***` as password placeholder in a default. | CRITICAL |
+| C5 | `whatsapp_webhook.py:29` | **Same wrong Redis URL:** `redis://redis:***@postgres:5432/helpdesk` | CRITICAL |
+| C6 | `email_fetcher.py:83` | **Missing API endpoint:** POSTs to `/tickets/create` but no such route exists in `agent_server.py` — only `/chat` and `/health` are defined. Feature is broken. | CRITICAL |
+
+### 🟡 DEGRADED (Should Fix)
+
+| # | File | Issue | Severity |
+|---|---|---|---|
+| D1 | `rate_limiter.py` | **In-memory only:** Redis client is stored but never used. Rate limiting won't work across replicas/restarts. | DEGRADED |
+| D2 | `agent_server.py` | **Blocking calls in async:** `get_system_prompt()` (file I/O) and `rate_limiter.check_request()` are sync methods called from async endpoints. | DEGRADED |
+| D3 | `session_manager.py:92` | **O(N) `redis.keys()`:** Used in `get_active_count()` and `cleanup_expired()` — dangerous in production with many sessions. | DEGRADED |
+| D4 | `health_monitor.py:83` | **O(N) `redis.keys()`:** Same pattern as D3. | DEGRADED |
+| D5 | `analytics.py:10` | **Hardcoded password in URL:** `postgresql://helpdesk:***@postgres:5432/helpdesk` | DEGRADED |
+| D6 | `whatsapp_webhook.py:138` | **Import inside function:** `import re` should be at module level. | DEGRADED |
+
+---
+
+## 4. SECURITY AUDIT (GUARDIAN — Phase 3 Preview)
+
+| Check | Status | Notes |
+|---|---|---|
+| Default credentials | ❌ | `change_me` passwords throughout: JWT_SECRET, CHROMA_AUTH_TOKEN, WHATSAPP_WEBHOOK_SECRET, DB_PASSWORD, REDIS_PASSWORD |
+| HTTPS enforced | ❌ | Nginx listens on port 80 only (no 443 config). `docker-compose.prod.yml` exposes 443 but no TLS certs configured. |
+| CORS | ⚠️ | `allow_origins=["*"]` — acceptable for development, but not documented as such |
+| Secrets in repo | ✅ | `.env` in `.gitignore`, `*.pem`, `*.key` excluded |
+| Gitleaks clean | ✅ | No hardcoded secrets found in code |
+| Rate limiting | ✅ | Nginx + app-level rate limiting implemented |
+| Docker rootless | ⚠️ | No non-root user specified in Dockerfiles |
+| Content-Security-Policy | ✅ | Set in nginx.conf |
+| SBOM | ❌ | No SBOM (CycloneDX or SPDX) present |
+| Security.md | ✅ | Present with contact + disclosure policy |
+| Auth for admin | ⚠️ | `ADMIN_API_KEY` configured but no auth middleware seen in agent_server.py |
+
+---
+
+## 5. DOCKER STANDARD CHECK
+
+| Check | Status | Notes |
+|---|---|---|
+| Health checks | ✅ | Defined for all services |
+| Named volumes | ✅ | All volumes named |
+| `.dockerignore` | ❌ | **Missing** — `.env`, `.git`, `node_modules` could leak into build context |
+| Multi-stage builds | ❌ | Dockerfile is single-stage |
+| Image version tags | ⚠️ | `searxng:latest`, `n8n:latest` — not pinned |
+| Non-root user | ❌ | Root user used in all Dockerfiles |
+| Tailscale pattern | ❌ | Not implemented |
+
+---
+
+## 6. GITHUB STANDARD CHECK
+
+| Check | Status | Notes |
+|---|---|---|
+| Repo description | ✅ | Set |
+| Topics | ⚠️ | Could add more specific topics |
+| Branch protection | ⚠️ | Not verified (requires GH API) |
+| CODEOWNERS | ❌ | **Missing** |
+| Dependabot | ✅ | `.github/dependabot.yml` present |
+| Issue templates | ✅ | Bug report + feature request |
+| PR template | ✅ | Present |
+| CI workflows | ✅ | CI + CodeQL workflows present |
+
+---
+
+## 7. MISSING STANDARD FILES
+
+| File | Purpose | Status |
+|---|---|---|
+| `j1.yaml` | Pipeline registry metadata | ❌ Missing |
+| `INTENT.md` | Engineering intent (Phase -1 ORACLE) | ❌ Missing |
+| `.dockerignore` | Docker build context optimization | ❌ Missing |
+| `CHANGELOG.md` | Release history | ❌ Missing |
+| `CODEOWNERS` | PR ownership routing | ❌ Missing |
+| `pyproject.toml` / `setup.py` | Python package metadata | ❌ Missing |
+
+---
+
+## 8. PRODUCTION SCORE
+
+| Category | Weight | Score | Weighted |
+|---|---|---|---|
+| Security | 20% | 65 | 13.0 |
+| Architecture | 15% | 75 | 11.25 |
+| Documentation | 15% | 80 | 12.0 |
+| Testing | 15% | 55 | 8.25 |
+| Deployment | 10% | 78 | 7.8 |
+| Automation | 10% | 82 | 8.2 |
+| GitHub Quality | 10% | 85 | 8.5 |
+| Branding | 5% | 85 | 4.25 |
+
+**Total Score: 73.25 / 100 — `DEGRADED`** (threshold: 90)
+
+---
+
+## 9. RECOMMENDED ACTIONS
+
+### Immediate (CRITICAL fixes):
+1. Fix `self._sessions = {}` in `rate_limiter.py:64` (typo `()` → `{}`)
+2. Add `import requests` to `zammad.py`
+3. Fix SQL injection in `session_manager.py:38` — use parameterized query
+4. Fix Redis URLs in `health_monitor.py` and `whatsapp_webhook.py` (port 6379, proper placeholder)
+5. Add `/tickets/create` endpoint to `agent_server.py` or fix `email_fetcher.py` to use `/chat`
+
+### Short-term:
+6. Add `.dockerignore`
+7. Pin Docker image versions (no `:latest`)
+8. Fix blocking calls in async endpoints
+9. Replace `redis.keys()` with `SCAN` in session_manager and health_monitor
+10. Add `import re` at top of `whatsapp_webhook.py`
+
+### Medium-term:
+11. Create `j1.yaml` and `INTENT.md`
+12. Create `CHANGELOG.md`
+13. Add CODEOWNERS file
+14. Implement Redis-backed rate limiting (not just in-memory)
+15. Add non-root user to Dockerfiles

CHANGELOG.md

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+# Changelog
+
+All notable changes to CommandDesk will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+### Fixed
+
+- **CRITICAL:** Fixed `rate_limiter.py` dict initialization typo (`=()` → `={}`) that broke rate limiting entirely
+- **CRITICAL:** Added missing `import requests` to `zammad.py` — would crash on ticket operations
+- **CRITICAL:** Fixed SQL injection vulnerability in `session_manager.py` — replaced string formatting with parameterized query
+- **CRITICAL:** Fixed wrong Redis URLs in `health_monitor.py` and `whatsapp_webhook.py` (referenced PostgreSQL port 5432 instead of Redis port 6379)
+- **CRITICAL:** Fixed `email_fetcher.py` to route email-to-ticket through existing `/chat` endpoint instead of non-existent `/tickets/create`
+- Moved `import re` to module level in `whatsapp_webhook.py` (was inside function)
+- Removed hardcoded placeholder password from `analytics.py` default URL
+- Replaced `redis.keys()` with `SCAN` cursor iteration in `session_manager.py` and `health_monitor.py` to avoid O(N) blocking calls
+- Added `.dockerignore` to prevent build context leaks
+- Added `j1.yaml` for pipeline registry metadata
+
+### Changed
+
+- `session_manager.py`: `import uuid` moved to module level
+- `health_monitor.py`: Fixed Redis URL default to proper format
+- `whatsapp_webhook.py`: Fixed Redis URL default to proper format
+- `analytics.py`: PostgreSQL URL default now empty (must be set via env)