FIX Issue#548 Update Loader: INCLUDED? doesn't work properly with encapped Re

Removing `join encap-fs/base file` seems to attach 'none value to the beginning of the file name, so the file does not match properly with previously included files.

I tested this by encapping red and testing with Kaj's SDL examples that were double including common.reds and failing to compile.  With this change, those files compiled without trouble.