Now passing options explicitly instead of using implicit @options
simplified Pipeline so it works with run_enumerate
and with run_fork
simplified read/write_fastq
simplified command dump
simplified command assemble_pairs
simplified command clip_primer
simplified command trim_primer
simplified command trim_seq
simplified command mean_scores
simplified command grab
simplified command plot_histogram
fixed status_track
simplified command plot_scores
all commands work again
removed redundant add method and added fork option
added records_in and records_out to all commands
work on status and progress
all tests green
fixed div warnings