WinMerge Portable Development

I wanted to make WinMerge Portable but I have some issues on how I would treat the registry entries.

I skimmed the source code of winmerge and found the following entries which rely on the registry. (note that WinMerge, uses a Wrapper, CRegKeyEx at ReyKey.h/cpp)

VssPrompt.cpp: line 97 <-- checks/injects into Visual source safe
SourceControl.cpp: line 123 <-- ditto
PropRegistry.cpp: lines 185 and 146 <-- settings are stored here
Plugins.cpp: line 77 <-- checks for windows scripting host

I know what to do with PropRegistry (just reroute it). However, what should I do with the rest?