added .gitignor for env config files
removed input set support, changed set types to reflect class case format. removed some analysis methods which are now availale from the sets and have been superceded by more specific analysis type params. made cell type optional
changed set type to match class case, removed input set support, implemented get_alignment_files_by_ResultSet_formats, changed init_branch_config to init_branching_by_analysis and now flows correctly using branch_job_groip