Update model visibilty logic

Simplifies the logic for setting model visibility and updates it work correctly when adding or removing a stage from the project. Most notably, this version of pqACE3PStages no longer depends on pipeline resources being in memory when switching stages.

The branch includes several other updates: (i) updates the job-submit logic in qtStagesWidget to always ask user to confirm before deleting a stage (previous version only did that if the stage contained job data); (ii) checks export operation result before submitting ACDTool jobs; (iii) checks for results directory overwriting data from a previous stage and asks user to confirm before submitting job.