Move thermal code out of trapp/run.py

Created by: sinkap

We should think of moving functions like plot_all_freqs plot_freq_hists to a specific module or have another class that inherits trappy.Run which is thermal specific. We can even have such code in bart.thermal and move all subsystem specific code to their respective subsystem in BART.

Please share your thoughts on this as well? Considering existing dependencies and backward compatibility.