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>

Makefile

@@ -0,0 +1,48 @@
+.PHONY: help setup run test test-unit test-integration lint typecheck clean
+
+VENV := .venv
+PYTHON := $(VENV)/bin/python
+PIP := $(VENV)/bin/pip
+PYTEST := $(VENV)/bin/pytest
+RUFF := $(VENV)/bin/ruff
+MYPY := $(VENV)/bin/mypy
+UVICORN := $(VENV)/bin/uvicorn
+
+HOST := 0.0.0.0
+PORT := 8777
+
+help: ## Show this help
+	@grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | sort | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-20s\033[0m %s\n", $$1, $$2}'
+
+setup: ## Create venv and install all dependencies
+	python3 -m venv $(VENV)
+	$(PIP) install --upgrade pip
+	$(PIP) install -e ".[dev]"
+
+run: ## Start the development server on port 8777
+	@mkdir -p build/logs
+	@if lsof -Pi :$(PORT) -sTCP:LISTEN -t >/dev/null 2>&1; then \
+		echo "Error: Port $(PORT) is already in use"; \
+		echo "Run: lsof -i :$(PORT) to see what's using it"; \
+		exit 1; \
+	fi
+	$(UVICORN) src.main:app --reload --host $(HOST) --port $(PORT) 2>&1 | tee build/logs/server.log
+
+test: ## Run unit tests (no external services needed)
+	$(PYTEST) --ignore=tests/e2e --ignore=tests/integration
+
+test-unit: test ## Alias for test
+
+test-integration: ## Run integration tests (needs Claude/Ollama)
+	$(PYTEST) tests/agents/test_tatlock_agent.py -v
+
+lint: ## Run ruff linter and formatter check
+	$(RUFF) check src tests
+	$(RUFF) format --check src tests
+
+typecheck: ## Run mypy type checking
+	$(MYPY) src
+
+clean: ## Remove build artifacts, caches, and coverage reports
+	rm -rf .cache build
+	find . -type d -name __pycache__ -exec rm -rf {} + 2>/dev/null || true