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Please check my today's change in SourceFoldersPanel and do something similar in your panel. Search for "FreeformProjectGenerator.relativizeLocation" - you should use it to relativize paths. Easy to fix.
Dupe, I think.
Sorry, missed the "web" part, presumably not a dupe.
will look at it, I think I submitted something like this against web some time ago, too
Fixed in trunk - used the relativizeLocation() method in web panel, too.