refactor: consolidate project structure and clean up documentation

- Move docs to docs/ (philosophy, roadmap, orchestration scenarios,
  claude integration, testing improvements)
- Strip completed phases from roadmap and claude integration docs
- Move dependencies from requirements*.txt into pyproject.toml
- Move pytest config from pytest.ini into pyproject.toml
- Add Makefile replacing wakeup.sh (setup, run, test, lint, etc.)
- Add CI test gate in Gitea Actions workflow
- Consolidate caches into .cache/ (pytest, mypy, ruff)
- Consolidate build output into build/ (coverage, logs)
- Update Dockerfile for pyproject.toml install
- Update cross-references in README, AGENTS.md, CLAUDE.md

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

README.md

@@ -1,6 +1,6 @@
 # Tatlock - Your Homelab Butler
 
-> **📖 For the complete system vision and architectural philosophy, see [PHILOSOPHY.md](PHILOSOPHY.md)**
+> **📖 For the complete system vision and architectural philosophy, see [docs/philosophy.md](docs/philosophy.md)**
 
 A privacy-first, offline-capable personal assistant system that coordinates specialized AI agents to help with research, development, home automation, and daily organization.
 
@@ -89,12 +89,8 @@ A privacy-first, offline-capable personal assistant system that coordinates spec
 git clone https://git.schweitz.net/jpmschweitzer/tatlock.git
 cd tatlock
 
-# Create virtual environment
-python -m venv .venv
-source .venv/bin/activate  # Windows: .venv\Scripts\activate
-
 # Install dependencies
-pip install -r requirements.txt
+make setup
 ```
 
 ### Run the Server
@@ -396,8 +392,7 @@ tatlock/
 │   │   └── multi_tenancy.py # User isolation utilities
 │   └── main.py              # Application entry point
 ├── tests/                   # Comprehensive test suite
-├── PHILOSOPHY.md            # System vision and architecture
-├── IMPLEMENTATION_ROADMAP.md # Development phases
+├── docs/                    # Project documentation
 ├── CHANGELOG.md             # Version history
 └── README.md                # This file
 ```
@@ -416,8 +411,8 @@ For LLM agent development guidelines and architectural decisions, see [AGENTS.md
 
 ## Documentation
 
-- **System Philosophy**: [PHILOSOPHY.md](PHILOSOPHY.md) - Vision, goals, and architectural patterns
-- **User Guide**: This file - Installation, usage, and examples
+- **System Philosophy**: [docs/philosophy.md](docs/philosophy.md) - Vision, goals, and architectural patterns
+- **Development Roadmap**: [docs/roadmap.md](docs/roadmap.md) - Open work and planned phases
 - **Developer Guidelines**: [AGENTS.md](AGENTS.md) - LLM agent development patterns
 - **Version History**: [CHANGELOG.md](CHANGELOG.md) - Changes and releases