Dependencies of filtered files are not considered

[AndyOGo]

In case of someone uses a tool like metalsmith-branch to select all pug files, but exclude/filter one directory layouts.
Then if any pug file extends a file within layouts, this file wont relinquish it's dependencies, because it's not reachable from the files array.

One big hammer solution could be #7

[AndyOGo]

This can be workarounded by using paths option