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right now the current path for custom icons is defined in the FolderItems.xml file, like:
\$(Drive)\Path\to\wherever\the\icon\is\icon.ico,0

IMHO it would be much better if you could create a folder, let's say Data\custom-icons\ and then define the path to the icon like this:
..\custom-icons\icon.ico,0

This way the application and its customized icons could be really portable.