Removed source files related to P3 software

P3 is distributed with X!Tandem. But is a different
project, its code doesn't belong in rTANDEM.
Solution to bug #1 - problem using multiple fasta files

The conversion of the Rdata in deque was using only one out
of two values (probably on the model of the conversion to map).
That led X!Tandem to ignore some fasta files.
Corrected bug #2 - Problem with multithreading.

It was actually a faulty message that caused R to
crash, and not multithreading per se.