Files being deleted from other plugins

[Cameron]

I'm not 100% sure if it is the case, but it seems as if permalinks is replacing folders with the permalink structure defined in a given linkset. For example:

When I run a pagination plugin:

A directory is created with paginated post items like this;

blog/
  1/
    index.html
  2/
    index.html

I then want to permalink each post to be blog/2016/08/23/post-title-here, so I implement permalinks after:

{
        "match": { "collection": "posts" },
        "pattern": "blog/:date/:title"
      },

The result is a single folder:

blog/
   2016/
      08/
        23/
          post-title-here/
            index.html

How can I fix this?

[Cameron]

Yep, I think this is it: https://github.com/segmentio/metalsmith-permalinks/blob/master/lib/index.js#L93