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>

.gitignore

@@ -46,27 +46,32 @@ ENV/
 .ipynb_checkpoints/
 *.ipynb
 
-# Testing & Coverage
+# Caches (pytest, mypy, ruff)
+.cache/
+
+# Build output (coverage, logs)
+build/
+
+# Legacy cache/output locations (in case tools fall back)
 .pytest_cache/
+.mypy_cache/
+.ruff_cache/
 .coverage
-.coverage.*
 coverage.xml
 htmlcov/
+
+# Testing
 .tox/
 .nox/
 *.cover
 .hypothesis/
 
 # Type checking
-.mypy_cache/
 .dmypy.json
 dmypy.json
 .pyre/
 .pytype/
 
-# Linting
-.ruff_cache/
-
 # Logs
 logs/*
 !logs/traces/