- Updated the `_print_checks` function to replace console prints with logging functions for better traceability.
- Introduced timing functionality in the `doctor`, `dry_run`, and `up` functions to log the duration of preflight checks.
- Modified the `wait_ssh` function to accept a logging callback, improving SSH wait feedback.
- Enhanced the `mark` method in `PhaseTimes` to log phase durations, aiding in performance analysis.
- Updated various remote scripts to ensure error messages are printed to stderr for better error handling.