Fixed error from unrecognized arguments

[jordansafer]

Got the following error from the example/template:

usage: mutatex [-h] [-a] [-u] [-n NRUNS] [-p NP] [-m MUTLIST] [-q POSLIST] [-S] [-s] [-x FOLDX_BINARY]
               [-b ROTABASE] [-f {suite4,suite5}] [-l] [-R REPAIR_RUNFILE_TEMPLATE]
               [-M MUTATE_RUNFILE_TEMPLATE] [-I INTERFACE_RUNFILE_TEMPLATE] [-B]
               [-C {partial,deep,none}] [-c] [-L] [-v]
               PDBFILE [PDBFILE ...]
mutatex: error: unrecognized arguments: --clean-deep --skip-check

One option is to replace --clean-deep with -C deep, instead of removing it, I could do that and update the other examples as well with whatever makes the most sense!

[mtiberti]

Hi, thank you! Yes - I think the issue here is that we first set up these examples using an older version of mutatex. Looks like a good proposed fix. I had a look and it seems to me that none of the others have this problem - or have you noticed something else?

[jordansafer]

You're right. This is the only example with the issue. I updated with the fix

[mtiberti]

Looks great, thank you! I think we can merge this