The directory dir specified in the error message was specified as an emake root, but that location is covered by the directory other dir, so it is redundant.
During startup emake performs a series of validation checks on the directories specified as emake roots. As part of the validation process emake checks whether any of the directories specified are subdirectories of any other directory specified as an emake root. If any such redundant entries are found, emake will display this warning and proceed as if the redundant directory had not been specified as an emake root.
This message is displayed if the user specifies two directories as emake roots such that one directory is contained within the other directory. For example, the user might specify both /foo/bar/baz and /foo as emake roots, but /foo/bar/baz is contained within /foo.