refactor: make repo Composer-compatible by moving php/ to root and ref/ to doc/reference_samples
- Move src/, tests/, bin/, generated/, proto/, composer.json, composer.lock, phpunit.xml from php/ to repo root
- Move ref/ to doc/reference_samples/ for better organization
- Remove vendor/ from git tracking (now properly gitignored)
- Update all test file paths (dirname adjustments and ref/ -> doc/reference_samples/)
- Update all documentation paths (AGENTS.md, doc/*.md)
- Remove php.bak/ directory
- All 252 tests pass
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