Added functions to startup script, including synonymns for different commands

Grouped all variables related to HTGT_MIGRATION_ROOT together in set_htgt_paths
Fixed issue with gene index checking

Removed WellSummaryByDI reference in Projects.pm
tidied up project_rs query in report.pm by removing join syntax (not necessary with prefetch)
and referencing new_ws_entries (NewWellSummary) instead of ws_by_di_entries (WellSummaryByDI).