Add better exception handling in transition list input - in particular make the FileModifiedException more informative#3202

bspratt wants to merge 7 commits intomasterProteoWizard/pwiz:masterfrom

Skyline/work/20241018_handle_skyd_changed_in_associate_proteinsProteoWizard/pwiz:Skyline/work/20241018_handle_skyd_changed_in_associate_proteinsCopy head branch name to clipboard