Fix -clusters options from the CLI

[althonos]

Hi!

As reported by @vagkaratzas in althonos/pytrimal#5 it seems that the -clusters issue from the CLI doesn't work as expected, as even example runs seem to always return the full alignment rather than the cluster representatives.

Digging a bit into this, I noticed that the Cleaner::getCutPointClusters was returning +inf as the identity cut point, which was causing all sequences to be selected. In several places of the function code, variables were not properly initialized and/or reinitialized, which was causing inconsistent behavior across executions, followed by a division-by-zero which was causing +inf to be returned.

I fixed the Cleaner::getCutPointClusters code so that now the -clusters option works as expected. In addition, I added some missing #include statements which were preventing the project from compiling with GCC 15.2.1, at least on my machine.

[althonos]

Thanks @scapella !

[scapella]

Thanks for your contributions to the code. It has been a long time since I wrote that code, and those fixes seem obvious to me now :-)