variety of syntax fixes
update get_stage_order()
syntax fixes
added existence checks for imageprep stage
added existence check of commands[] in imageprep - if stage is complete then commands list will be empty, dont add stage to stage order/list
changed number of imageprep commands running in parallel from 1 to 4
added bestlinreg for prep stage
bash script file for imageprep stage
fixed name of bestlinreg to bestlinreg.pl
more testing