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I am using WinMerge to compare .rtf files using CompareMSWordFiles plugin. (One can just change .docx extension to .rtf to test the issue.) With an older version (2.16.36.0) it worked just fine. With newer version 2.16.44.0, for every compared .rtf file there pops a Convert File dialog window requiring to confirm the 'Convert file from:' Rich Text Format (RTF). This makes it very inconvenient to compare .rtf files. This is a Word setting that can be found in Word Options > Advanced > General > Confirm file format conversion on open, which is normally disabled, but is enabled when using the plugin.
I am not a programmer, but I believe the issue is in WinMerge\MergePlugins\CompareMSWordFiles.sct where it has the following line in two (2) places
var doc = wd.Documents.Open(fileSrc2, -1, -1)
The second parameter is for 'ConfirmConversions' with -1 defaulting to 1/True. I believe it should be as below thus using the current setting, rather than turning it on or off, though I am not able to verify it on the system I use WinMerge on: