Extract annotation_build method
Extract script_path method
Extract method to resolve format and input file
Merge branch 'updated' into gb_master
Remove trailing whitespace.
Update test to have less trailing whitespace.
updated jenkins submodule to ad170e0
updated jenkins submodule to ffac64e
updated jenkins submodule to 8c8edaa
updated jenkins submodule to b9e8e79
Do all the sorting and filtering logic even if from an Analysis Project

This change is pursuant to RT#98634.
updated jenkins submodule to 8363e5f
updated jenkins submodule to c81b2ba
Move string args tweaking into subroutine
Make accessor functions rather than local variables
Extract custom_args method
Extract methods for plugin_args and cache_args
Extract method for db_connect params
Extract methods to construct and run the command
Extract method to get or create the temp dir