It's a simple question, yet for the life of me, can't find a simple answer to this question.
Clear the "Where to build the binaries" history in cmake gui
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I don't believe there is a way to clear the cached build paths through the CMake GUI nor through the command line interface; however, in windows you can use the registry editor and navigate to HKEY_CURRENT_USER/SOFTWARE/Kitware/CMakeSetup/Settings/StartPath. There, you'll see some indexed variables prefixed by "WhereBuild". You can modify these paths or delete them entirely.
On OS X, these variables are stored in a properties list located in $HOME/Library/Preferences/com.kitware.CMakeSetup.plist.
On other Unix/Linux-based systems, you may find it in $HOME/.config/Kitware/CMakeSetup.conf