Fix converting AUGUSTUS_CONFIG_PATH into AUGUSTUS_BASE
Fix converting AUGUSTUS_CONFIG_PATH into AUGUSTUS_BASE

This fixes an issue caused by AUGUSTUS_CONFIG_PATH having more than one 'config' substring, i.e. 'configfiles/augustus/config' getting converted to 'files/augustus/'.
nextgenusfs/funannotate,nextgenusfs/funannotate,nextgenusfs/funannotate,nextgenusfs/funannotate