That is only true for 3d models and symbols. footprints are not on your local machine. They are downloaded into some temporary storage (i don't know where) iff they are needed. (Via the github api)
Have a look in /usr/share/kicad/modules. This directory is empty! (exept from the packages3d directory which holds the 3d models.
This inconsistency is one of the major problems with the kicad library. If we update for example the scaling of a 3d model to be 1 instead of 1/2.54 the users get the new footprint with the new scaling factor immediately but they do not get the new 3d models.
This can be avoided by using the local setup. There is a tutorial out there written by @bobc https://github.com/bobc/kicad-doc/wiki/How-to-install-local-Footprint-libraries (notice that everything is done from within kicad. No package manager is involved.)
The parse error came from the fact that we updated the complete connectors_molex.pretty footprint lib. It had one defect footprint in it.
If eeschema crashed for another reason, than this is another bug. I'm only writing about the bug you told us in the first post or more precisely in the title of this topic. (I can only answer to questions that have been stated clearly and for whom i have enough information.)