Update docs to reflect the centralized config.AgentEnv() function and
complete environment variable coverage:
reference.md:
- Restructured env vars section with tables by category
- Added GT_ROOT, GT_CREW, BEADS_AGENT_NAME documentation
- Added "Environment by Role" quick reference table
- Added doctor check documentation for env-vars validation
identity.md:
- Updated Environment Setup section with complete examples
- Added crew environment example showing BEADS_NO_DAEMON
- Mentioned centralized config.AgentEnv() function
- Cross-referenced to reference.md for full details
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>