Install MIRA 4.0 RC3
Adjust MIRA4 output filenames for mapping...
Insert MIRA manifest into log file; report time in hours
MIRA 4.0 RC3 does allow explicit file format declaration

We can drop the FASTQ symlinking (which would/should have broken
with MIRA input reads, or a FASTA backbone) now.

Next, declare the format in the manifest itself...
Tell MIRA4 file types via manifest