Feature Request: Centralize logging strategy and implement multiple log levels

[poiley]

Centralize logging using a single config (e.g. Python’s logging module), and support multiple log levels (DEBUG, INFO, WARNING, ERROR, CRITICAL). Refactor current logging to use this system. Add options to control verbosity and output destinations. Document usage.

[poiley]

Scope of issue expanded to log output directory configuration and detached monitoring of analysis