I can then programmatically choose which file to import with importlib. Is there a way to tell clearml programmatically to analyze the files, so it can built up the requirements correctly?

Sadly no 😞
It analyzes the running code, then if it decides it is not a self contained script it will analyze the entire repo ...

I just saw that 

Task.create

 takes

Task.create is Not Task.init. It is meant to allow you to create new Tasks (think Jobs) from your own code. A good example would be pipelines and automation where you want to create Tasks from a known codebase and send them for execution
BTW: any reason why you would not want to analyze the entire repo?