As of version 2.16.13, WinMerge now has support for settings stored in an INI file:
While, by default, it looks for an INI file next to the WinMergeU.exe file, you can also specify the INI file to use via command line:
Are there any plans to use this new functionality for the settings storage in the PortableApps.com version? It would be nice to not have to copy back and forth from the registry, but use a file that just sits in the \Data folder the whole time.
I'm not sure how the registry > INI file translation would take place, I've done a few tests and cannot get it to automatically populate the INI with the registry settings.
During my testing, I also noticed that it looks for a WinMerge.reg file next to WinMergeU.exe too. And it appears to read that on startup and write back to it on close. I don't see any option to define it's location using a command line option though.