Notice that an anime girl holding a programming book is in itself a (mild) subversion of gender roles. The stereotypical programmer is male, and the stereotypical programmer is not cute.
(I'm kinda repeating myself in this thread a bit, sorry but...) I can guarantee you that the anime girls holding programming books has been a thing for at least a decade, so the 2017 creation of that repository doesn't really mean much. Not sure about the programming sock meme but I think it's a bit more recent. However I do think it generates from certain "battlestation threads" on /g/ where people used to post photos of themselves sitting at their PC with those knee-high socks on and the meme kinda spread from there. Way before that screenshot itself.
Makes perfect sense that a meme combining anime and programming would come from 4chan's technology board.
I suppose what made the meme interesting enough to spread is the subversion of the traditional hacker aesthetic. Having a beard voluminous enough to carry The C Programming Language inside everywhere you went was a sign of great experience and wisdom. As a bonus, it also horrified "the suits", who were hackers' natural outgroup.
In the 21st century you just can't annoy the suits the same way because even large corporations don't demand people wear literal suits anymore. Baffling the HN crowd is what passes for iconoclasm these days.
Memes ensued
I don't think that is going on here, you have to consider that the anime girl is holding the book towards the viewer, my guess is that the implication is supposed to be "Will you explain it to me".
This is not correct. It's hard to explain if you've never seen them in context but rather than "will you explain it to me" they are actually saying "won't you read this?" or "will you learn this language for me?" kinda note. They used to be commonly posted as OP image in programming threads on /g/ with lines like "have you read sicp today /g/?" or similar. There's also another very common variation of this meme for gamedev communities on 4chan with the girl from the anime New Game (see this[0] clip, I couldn't find the meme itself) with a similar vibe.
? Why? There's nothing that indicates this, the history behind these images shows the clear opposite. This to me sounds more like your (unconscious?) biases are showing more than it actually being a thing. Trust me, it's not really how this meme works. If you actually look at most images in that repo the girls are either reading the book, explaining the book, or clearly pushing it (often aggressively) towards the viewer to make them read it.
EDIT: Are you familiar with Serial Experiments Lain? I think that was one of the first ones to pop up with these.
Reflecting upon my own impressions and how these changed, I am more conscious of these points and find it hard to ignore them. Assuming that I am not totally mistaken, which of course might be the case, knowing that others don't see these things pains me. More so when someone like the author of the link publically stands by it.
But you are right though that not every image is like this.