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.Xresources triggers regeneration of directory when not needed

When visiting my home directory, the file .Xresources isnt seen as being a member of the directory contents despite being a member. The problem lies with the functions subdirectories-up-to-date and make-paths-list. I am at a loss as to what is going wrong, as it seems that it should be returning true. I'm not sure if its due to the specific file .Xresources or if its just the first hidden file thats triggering the error.

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