👌 IMPROVE: Updated section on running calculations (#366)

Major revamp of the "Running calculations" section:

* Removed all things related to troubleshooting (moved to a different module, see #353 )
* Changed introduction to highlight the contrast between how data is organized when running normally vs running with AiiDA. This is in hope that it'll illustrate more explicitly "how to do with AiiDA the things I already know how to do on my own".
* Separated main content into 2 main sections: preliminary setups (which are performed using verdi CLI) and preparing the calculation (which is performed using the verdi shell). This is to address the problem we typically have of people needing to go back and forth from bash to python.