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refactor: comprehensive repository cleanup (Phases 1-7) #35

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ad1123a
feat: consolidate network configuration and fix security issues (Phas…
sygint Jan 22, 2026
d7e76fc
docs: consolidate documentation - delete root-level duplicates (Phase 2)
sygint Jan 22, 2026
bd004d4
chore: clean up root directory - delete temp files and relocate mispl…
sygint Jan 22, 2026
f1e70f3
refactor: centralize configuration and remove duplicates (Phase 4)
sygint Jan 22, 2026
a728034
refactor: clean up unused modules and improve organization (Phase 5)
sygint Jan 22, 2026
6d505c6
chore: remove unused Kanboard scripts (Phase 6)
sygint Jan 22, 2026
b32df7d
refactor: use fleet-config in deploy.nix and clean up stale files (Ph…
sygint Jan 22, 2026
658b166
docs: add TODO for remote repo size optimization
sygint Jan 22, 2026
ad51449
docs: add research TODO for alternative Wayland compositors and shells
sygint Jan 22, 2026
6ed464d
docs: update BOOTSTRAP.md to reference fleet-config.nix
sygint Jan 22, 2026
878c14c
docs: delete completed cleanup documentation (Phase 8)
sygint Jan 22, 2026
13caca9
docs: add nixos-fleet migration plan
sygint Jan 22, 2026
3f38b0f
docs: add nixos-fleet readiness analysis
sygint Jan 22, 2026
80a4829
docs: cleanup fleet documentation (Phase 8 final)
sygint Jan 22, 2026
9542786
feat: add nixos-fleet as flake input (Phase 1)
sygint Jan 22, 2026
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17 changes: 12 additions & 5 deletions DOCS.md
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Expand Up @@ -7,7 +7,7 @@ Complete guide to this NixOS configuration. Start here for navigation.
**New to this config?** Start here:
1. Read [README.md](README.md) - Project overview and quick start
2. Check [FLEET-MANAGEMENT.md](FLEET-MANAGEMENT.md) - How to deploy systems
3. Review [docs/SECURITY.md](docs/SECURITY.md) - Security baseline
3. Review [docs/security/SECURITY.md](docs/security/SECURITY.md) - Security baseline

## 📚 Core Documentation

Expand All @@ -19,7 +19,7 @@ Complete guide to this NixOS configuration. Start here for navigation.
| [FLEET-MANAGEMENT.md](FLEET-MANAGEMENT.md) | Deploy and manage multiple NixOS systems | Initial deployment, routine updates |
| [docs/BOOTSTRAP.md](docs/BOOTSTRAP.md) | Bootstrap new NixOS systems from scratch | Installing NixOS on new hardware |
| [systems/cortex/AI-SERVICES.md](systems/cortex/AI-SERVICES.md) | AI/LLM infrastructure on Cortex (Ollama, NVIDIA) | Using AI services, GPU troubleshooting |
| [docs/SECURITY.md](docs/SECURITY.md) | Security configuration (fail2ban, auditd, SSH) | Hardening systems, security audit |
| [docs/security/SECURITY.md](docs/security/SECURITY.md) | Security configuration (fail2ban, auditd, SSH) | Hardening systems, security audit |
| [SECRETS.md](SECRETS.md) | Complete secrets management guide with sops-nix | Managing passwords, API keys, certificates |

## � Planning & Implementation
Expand All @@ -29,7 +29,7 @@ Complete guide to this NixOS configuration. Start here for navigation.
| [docs/PROJECT-OVERVIEW.md](docs/PROJECT-OVERVIEW.md) | Architecture, philosophy, system details | Understanding design decisions |
| [docs/ROADMAP.md](docs/ROADMAP.md) | Implementation roadmap and timeline | Planning next features |
| [docs/IMPLEMENTATION-GUIDE.md](docs/IMPLEMENTATION-GUIDE.md) | Step-by-step implementation guides | Adding new features |
| [docs/TODO-CHECKLIST.md](docs/TODO-CHECKLIST.md) | Progress tracking and status | Tracking what's done |
| [docs/planning/TODO-CHECKLIST.md](docs/planning/TODO-CHECKLIST.md) | Progress tracking and status | Tracking what's done |

## �🛠️ Troubleshooting & Reference

Expand Down Expand Up @@ -95,11 +95,18 @@ When updating documentation:
│ ├── PROJECT-OVERVIEW.md # Architecture & philosophy
│ ├── ROADMAP.md # Implementation timeline
│ ├── IMPLEMENTATION-GUIDE.md # Step-by-step guides
│ ├── TODO-CHECKLIST.md # Progress tracking
│ ├── ARCHITECTURE.md # Module system docs
│ ├── SECURITY.md # Security configuration
│ ├── BOOTSTRAP.md # Bootstrap new systems
│ ├── FLEET-FUTURE.md # Future fleet tools (Colmena)
│ ├── planning/ # Planning & tracking docs
│ │ ├── TODO-CHECKLIST.md # Progress tracking
│ │ ├── CLEANUP-PRD.md # Cleanup project details
│ │ └── CLEANUP-CHECKLIST.md # Cleanup tasks
│ ├── security/ # Security documentation
│ │ ├── SECURITY.md # Security configuration
│ │ ├── SECURITY-ROADMAP.md # Security roadmap
│ │ ├── SECURITY-SCANNING.md # Secret scanning
│ │ └── CORTEX-SECURITY.md # Cortex hardening
│ ├── troubleshooting/ # Specific issue guides
│ └── blog/ # Learning journey posts
└── systems/
Expand Down
12 changes: 6 additions & 6 deletions ISSUES.md
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Expand Up @@ -143,7 +143,7 @@
- Options: `nixos-rebuild build-vm`, `machinectl`, Proxmox VMs
- Related: `machines` NixOS feature, `systemd-nspawn`
- Tags: `testing`, `vms`, `dev-environment`
- See: [TODO-CHECKLIST.md](./docs/TODO-CHECKLIST.md) - Testing & Validation section
- See: [TODO-CHECKLIST.md](./docs/planning/TODO-CHECKLIST.md) - Testing & Validation section

### Security Tooling

Expand All @@ -162,7 +162,7 @@
- Impact: Deep historical secret detection in git history
- Solution: Available in devenv (v3.90.9), convenience script created
- Usage: `./scripts/security-scan.sh [quick|full|history]`
- Documentation: `docs/SECURITY-SCANNING.md`
- Documentation: `docs/security/SECURITY-SCANNING.md`
- Location: `devenv.nix`, `scripts/security-scan.sh`
- Tags: `security`, `git`, `secrets`

Expand Down Expand Up @@ -255,7 +255,7 @@
- Solution: Pre-commit hooks active, convenience script created, comprehensive documentation
- Tools: git-secrets (pre-commit) + TruffleHog v3.90.9 (manual/CI)
- Scripts: `scripts/security-scan.sh`, `scripts/git-hooks/pre-commit`
- Documentation: `docs/SECURITY-SCANNING.md`
- Documentation: `docs/security/SECURITY-SCANNING.md`
- Impact: Prevents accidental secret commits and enables deep historical scanning

---
Expand Down Expand Up @@ -283,15 +283,15 @@

### Related Documentation

- [TODO-CHECKLIST.md](./docs/TODO-CHECKLIST.md) - Implementation roadmap
- [TODO-CHECKLIST.md](./docs/planning/TODO-CHECKLIST.md) - Implementation roadmap
- [ARCHITECTURE.md](./docs/ARCHITECTURE.md) - System architecture
- [FLEET-MANAGEMENT.md](./FLEET-MANAGEMENT.md) - Deployment workflows
- [SECURITY.md](./docs/SECURITY.md) - Security configuration
- [SECURITY.md](./docs/security/SECURITY.md) - Security configuration

---

**Notes:**
- Review and update this file weekly
- Move stale items to backlog or archive
- Keep critical issues visible at the top
- Cross-reference with TODO-CHECKLIST.md for implementation tasks
- Cross-reference with docs/planning/TODO-CHECKLIST.md for implementation tasks
4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -16,7 +16,7 @@ Personal NixOS configuration with **unified feature modules** based on the dendr
- **[docs/BOOTSTRAP.md](docs/BOOTSTRAP.md)** - Bootstrap new NixOS systems

**Security & Secrets:**
- **[docs/SECURITY.md](docs/SECURITY.md)** - Security configuration
- **[docs/security/SECURITY.md](docs/security/SECURITY.md)** - Security configuration
- **[SECRETS.md](SECRETS.md)** - Secrets management (sops-nix + age)

## 🚀 Quick Start
Expand Down Expand Up @@ -257,5 +257,5 @@ Some extensions are already configured but commented out. To enable them:
## 📋 Notes

- Dotfiles are managed using Home Manager with live-updating symlinks
- Monitor configuration is stored in `monitors.json`
- Monitor configuration is stored in `systems/orion/monitors.json`
- Additional notes in `notes.txt`
25 changes: 0 additions & 25 deletions build.log
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18 changes: 9 additions & 9 deletions docs/BOOTSTRAP.md
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Expand Up @@ -71,10 +71,10 @@ OPTIONAL:

### Centralized Configuration Pattern

All host configurations use a centralized network topology defined in `network-config.nix`:
All host configurations use a centralized network topology defined in `fleet-config.nix`:

```nix
# network-config.nix - Central source of truth for all hosts
# fleet-config.nix - Central source of truth for all hosts
{
hosts = {
orion = {
Expand Down Expand Up @@ -102,16 +102,16 @@ All host configurations use a centralized network topology defined in `network-c
### System Variables Pattern

Each host has a `systems/<hostname>/variables.nix` file that:
- Imports from centralized `network-config.nix`
- Imports from centralized `fleet-config.nix`
- Defines machine-specific settings (user preferences, applications, etc.)
- Re-exports network config for convenient access
- Re-exports fleet config for convenient access

**Example:**

```nix
let
networkConfig = import ../../network-config.nix;
thisHost = networkConfig.hosts.orion;
fleetConfig = import ../../fleet-config.nix;
thisHost = fleetConfig.hosts.orion;
in
{
system = {
Expand Down Expand Up @@ -389,7 +389,7 @@ The `fleet.sh` script auto-loads host configuration from your Nix config:

### Wake-on-LAN

If configured in `network-config.nix`:
If configured in `fleet-config.nix`:

```bash
# Wake a sleeping host
Expand Down Expand Up @@ -576,7 +576,7 @@ ssh-add -l
- Note the IP address

2. **Configure the host**
- Add entry to `network-config.nix`
- Add entry to `fleet-config.nix`
- Create `systems/<hostname>/` directory with configuration
- Create `systems/<hostname>/variables.nix`
- Create `systems/<hostname>/disk-config.nix`
Expand Down Expand Up @@ -680,6 +680,6 @@ done

---

**Last Updated:** October 29, 2025
**Last Updated:** January 22, 2026
**Pattern Source:** EmergentMind's nix-config
**Status:** Active deployment method for all fleet systems
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