Hi,
I don't know if I understand well your feedback.
Malinette-soft includes last Pd.0.49 inside. The script "start-malinette-sh" must be launched by a Terminal or simply by Right Click > Open With > Other Application ... > Terminal, not with Pd or Purr-Data.
Or it seems that Gem is not loaded correctly. You could download it via "Help > Find externals" and replace it in "malinette-soft-master/externals/Gem" to see if it is ok.
You could use your own Pure Data of course with the "malinette-ide" flavor, but you will need to include all libraries. See "malinette-soft-master/malinette-ide/INSTALL.md"
Best.