To filter comments like <!-- smth with linebreaks --> in WinMerge:

1. Go to C:\Program Files (x86)\WinMerge, open IgnoreSectionMarkers.ini file
2. Delete everything that is there.
3. Put next lines in the file:


[set0]
StartMarker=<!--
EndMarker=-->
InlineMarker=<!--
FileType0=xml
FileType1=config

4. Save file and restart WinMerge.

To make these changes take effect, you need also next changes to WinMerge options:

"Compare" section: 

• disable "Match similar lines" checkbox
• enable "Filter comments" checkbox