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>

Dockerfile

@@ -5,8 +5,8 @@ WORKDIR /app
 RUN apt-get update && apt-get install -y curl \
     && rm -rf /var/lib/apt/lists/*
 
-COPY requirements.txt pyproject.toml ./
-RUN pip install --no-cache-dir -r requirements.txt
+COPY pyproject.toml ./
+RUN pip install --no-cache-dir .
 
 COPY src/ ./src/