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I've copied it back into the master branch of COLORE for now... I think Michael might've created separate definition CLIF files for each of the defined relations -- I know that there's been some discussions about having individual CLIF files for definitions, but I'll have to double check with him to see if we need to update the imports for all of the files you've listed.
in occupy/definitions/occupy_def.clif I changed the import
(cl-domain region (cl-imports http://colore.oor.net/mereology/mereology_def.clif))
to
(cl-domain region (cl-imports http://colore.oor.net/mereology/definitions/ppart.clif))
because no file mereology_def exists and only the ppart relation from the mereology is used.
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