stage 7 mosaicing, major clean up and modification to allow call from shell for jobs on NEX

mosaicing script shell script for job, modifications and clean up with comments

testing function mosaicing before shell script

turning script into shell callable code for stage 7 mosaicing

testing stage 7 mosaicing with layers options and temporary files removal

testing mosaicing stage 7 and fixing inputs

more changes to master script 7, stage 7 and testing

stage 7 mosaicing following assessment, script cleaned and integrated to workflow

mosaicing functions, option to remove temporary files

mosaicing functions, fixing outputs names and directories