I just upgraded from 3.0.1 to 3.1, lots of updates, thanks!
It looks to me however as if the stopwords node has a regression issue. I have configured a custom word list, but the terms are not removed from my Documents. I think this is a regression, as I am seeing unwanted words showing up that were not there before, and it only since I replaced the deprecated version with the new 3.1 verison.
To reproduce: it is a column containing non-tagged Documents. I have checked "replace column" and "ignore unmodifiable flag". I have left un-checked "case sensitive". I have tried different line endings in the custom file, and adding -tags, to no avail. I have even checked tried using the stopword list in the resources folder as a "custom file", which does not work.
Am I missing something?