docs: rewrite codebase architecture documentation

Complete rewrite of docs/codebase-architecture.md to fix corruption and update all module paths to match the current DDD architecture.

Fixed issues:
- Corrupted header with scrambled text from multiple sections
- Outdated paths referencing old structure (src/commands/, src/steps/, src/ansible/)
- Multiple duplicated sections throughout the file

Updated paths to match current architecture:
- src/application/commands/ (was incorrectly documented as src/commands/)
- src/application/steps/ (was incorrectly documented as src/steps/)
- src/infrastructure/external_tools/ansible/ (was incorrectly documented as src/ansible/)
- src/infrastructure/external_tools/tofu/ (was incorrectly documented as src/tofu/)
- src/infrastructure/external_tools/lxd/ (was incorrectly documented as src/lxd/)
- src/domain/environment/trace_id.rs (updated to reflect recent module move)

The documentation now accurately reflects the three-layer DDD architecture (Domain, Application, Infrastructure) with correct module paths and comprehensive descriptions.

Author: josecelano