latexindent formatting immediately overridden by Texify

[nealeyoung]

I am trying to use latexindent with some customization to indent for square braces. E.g.

[
  hi
]

I am able to get latexindent to do this by using a latexindent config file with these settings:

specialBeginEnd:
  specialBeforeCommand: 1
  squareBrackets:
    begin: \[
    end: \]
    lookForThis: 1

This works when I run latexindent on the file directly. However, when I run latexindent via pycharm via the "Code -> Reformat with latexindent" menu item, it doesn't work. (Text between brackets is not indented.) Checking the indent.log file shows that latexindent is indeed running correctly (and loading the customizations correctly). The only thought I have is that maybe, immediately after latexindent formats the file, texify is somehow reformatting it and removing the customized indenting. ?

Does anybody have any suggestions?