Add box generation for pythia + examples + fixes

[njacazio]

• Add seed to gun executable
• Checking output of custom gen running
• Update default config file
• Nuclei can be now be injected

[njacazio]

Ciao @preghenella, when you have time could you look at this PR? it introduces a box generator and the possibility to set the seed when using the particle gun.

[njacazio]

greenlight recieved, merging