pangenome arguments and temporary file

[RaphaelRaphael]

Hello,

As a novice user, I did lost a bit of time on a specific thing

PanACoTA pangenome -l UpdatedList_V4

it seems that the temporary file ViPa.All.prt should be used only when requested by the user and not by default. Alternatively, a warning could be added, since the -l UpdatedList_V4 option is no longer taken into account.