Working on the batch files for FragPipe I realized that we have two different ways of showing output for our Transition Settings changes:
1. Based on log output (best)
2. Structured but ad hoc for Full-Scan settings (should be changed to #1) - not even consistent in Full-Scan naming "full-scan" or "full scan"

Opening file...
File dia-fragpipe-template.sky opened.
Transition Settings -- Filter changed
Settings > Transition Settings -- Filter > Peptide Precursor charges changed from "2" to "2, 3, 4, 5, 6"
Settings > Transition Settings -- Filter > Ion types changed from "y" to "y, b, p"
Settings > Transition Settings -- Filter > Product ion selection start changed from "m/z > precursor" to "ion 3"
Settings > Transition Settings -- Filter > Product ion selection end changed from "3 ions" to "last ion"
Settings > Transition Settings -- Filter > Special ions: removed all
Transition Settings -- Instrument > Max m/z changed to "2000"
Settings > Transition Settings -- Instrument > Max m/z changed from "1500" to "2000"
Transition Settings -- Library changed
Settings > Transition Settings -- Library > Ion match tolerance changed from "0.5" m/z to "10" ppm
Settings > Transition Settings -- Library > Minimum product ions changed from "0" to "6"
Settings > Transition Settings -- Library > Product ions changed from "3" to "6"
Settings > Transition Settings -- Library > Pick changed from "From filtered ion charges and types" to "From filtered pr
oduct ions"
Changing full scan precursor isotope peaks to Count
Changing full scan precursor isotope peaks count to 3
Changing full scan acquisition method to DIA with isolation scheme 'Results only'
Changing full scan precursor mass analyzer to centroided
Changing full-scan precursor resolution to 10.
Changing full scan product mass analyzer to centroided
Changing full-scan product resolution to 10.
Changing full-scan extraction to +/- 2 minutes from MS/MS IDs.
Creating spectral library from files:
library.tsv.speclib

I am working on this. We simply need to move to ModifyDocumentWithLogging() for all our settings change arguments.

Fixed and released in 23.1.1.335