refactor logging?

We currently use a single logger `cwltool` instead of a module name based approach. Also the logging is always turned on instead of only when `cwltool.main.main()` is called

Start at cwltool.main.main() and trace where the single `cwltool` logger is configured and used across the package. Check how logging behaves when modules are imported versus when `main()` is called. Done means module-based loggers are used and logging is enabled only through `cwltool.main.main()`.

Written by the indexing model from the issue text.