Heavily rework and slightly fix the entire pggb script

[AndreaGuarracino]

This:

• reduces the entropy of the pggb script
• removes a few (not critical) bugs in the prefixes management
• fixes a few typos in the comments and the date in the log
• forces the current working directory as default output and temporary directories
• explicit the default values for the majority of the parameters, removing several instructions to manage them. In this way, we have in the log/YML file the values for all the parameters used in the run (for example, the kmer size and kmer threshold for wfmash were not explicitly reported in the first part of the log and in the YML file before).

[AndreaGuarracino]

Now we separate the mapping and alignment phases, managing the mapping file as a temporary file that can be kept for debugging purposes.