We previously had the same problem at University of Copenhagen, it was called "the hidden curriculum" among students.

When the undergraduate programme was reformed a few years ago these subjects where integrated into various courses, so they could be taught in a learning-by-doing fashion. As part of the first programming and problem-solving class (F#), we also teach LaTeX, Emacs and basic use of the command line, as part of a project-based software engineering course (second semester) Git is used extensively, and so on.