Trace auto generate I/O

[Cmheidelberg]

Describe the solution you'd like
At the moment mic encapsulate trace will find input and output files, but it wont add these to the mic.yaml until after the user runs the corresponding mic encapsulate inputs and mic encapsulate outputs commands. Trace should automatically assign inputs and outputs to the yaml (printing to terminal all automatically added i/o). Or at least there should be a option --auto that lets it automatically add i/o.

There could also be an option added to inputs and outputs commands that removes i/o from the yaml. Ex: mic encapsulate example_csv --remove. This would let users easily remove incorrectly added i/o

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