~/.hermes/
├── config.yaml           # Main configuration
├── .env                  # API keys and secrets
├── auth.json             # OAuth provider credentials
├── SOUL.md               # Agent identity (slot #1 in system prompt)
│
├── memories/
│   ├── MEMORY.md         # Persistent agent facts
│   └── USER.md           # User model
│
├── skills/               # All skills (bundled, hub, agent-created)
│   ├── mlops/
│   │   ├── axolotl/
│   │   │   ├── SKILL.md
│   │   │   ├── references/
│   │   │   └── scripts/
│   │   └── vllm/
│   ├── devops/
│   └── .hub/             # Skills Hub state
│
├── sessions/             # Per-platform session metadata
├── state.db              # SQLite session store with FTS5
├── cron/
│   ├── jobs.json         # Scheduled jobs
│   └── output/           # Cron run outputs
│
├── plugins/              # Custom plugins
├── hooks/                # Lifecycle hooks
├── skins/                # CLI themes
└── logs/                 # agent.log, gateway.log, errors.log