I don't think you can set up this kind of restriction.  However you could try setting a client convention to restrict the path in which files are indexed.  This would be a convention where Composer uploaded files should be stored, for example a new ~/Composer/ starting point.

You would have a convention like the following:

FileIndexer.Instance.Conventions.ForInstancesOf<UnifiedFile>()

.ShouldIndex(x => x.VirtualPath.StartsWith("Composer"));