docs: improve integration testing guide with directory indicators and new config workflow

- Add [PROJECT_ROOT], [TERRAFORM_DIR], [VM_REMOTE] indicators to all commands
- Document new template-based configuration system (Step 1.7)
- Add 'Working Directory Confusion' as most common troubleshooting issue
- Include configure-local and validate-config workflow steps
- Enhance directory context warnings and error recovery guidance
- Update summary to reflect new configuration workflow timing
- Fix markdown formatting and lint issues

Resolves the directory confusion issue encountered during testing where
make commands failed when run from wrong directory (infrastructure/terraform
vs project root).

Author: josecelano