Default to correct use of the configuration file

[vigji]

This will probably be solved in the testing branch, but
sashimi

from the terminal should just give the execution of whatever is set to be in the configuration, and should not require the additional inputs

sashimi --scanning ni

as is currently happening.

[diegoasua]

After we have merged #112 and #92 there will be a chance for a PR completely focused on command line entries, config file and thereof. Understandably, this sort of entry right now can be a source of annoyance. However, we must proceed in order. This will be addressed, alas, now it is not the time yet

[diegoasua]

@vigji is there something around the config file that we want to modify in the current entry status? I think the issue you were pointing to at the beginning was branch-specific . The only optional entry now is --scopeless (correct me if I am wrong)