Big fan of Tiddlywiki for its nonlinearity. You can see how it works without signing up or downloading anything; the site is itself an instance: http://tiddlywiki.com/
I second this. For me, anything with tagging and search would work. Mine lives in Dropbox (it runs in Firefox) so it's backed up and available on all my machines. A lot of the notes and ideas in it start out on paper (e.g. written on the go, or whenever the idea strikes me) so I get the benefits of paper. But rediscovery becomes essential as the volume of notes get large. Paper is ineffective because of the lack of search capability.
Neat - I'm in the process of making a similar system which will spit out Spigot plugins, with the aim of letting kids create some simple ones themselves and hopefully planting the seed for getting them interested in programming. As part of this I included a 'split screen' view showing the generated Java in addition to the normal block work area, though this is read-only.
It's been more of a challenge than I thought it would be to design the blocks such that the end set isn't near enough a 1:1 mapping to Java - showing it to a non-technical friend of mine made it clear that my intuition was way off. Would be interested to hear how you approached this (if you don't mind).
Also interesting that I didn't find your website when I was initially researching, though I did come across https://www.learntomod.com/ (and even that was hard to find). I suspect my base search term of "minecraft blockly" isn't the most common one used by the target market to find something for their kids though.
ServerBear did exactly this, though it seems they sadly shut down. ServerScope seems to do something similar - https://serverscope.io/ though without a huge breadth.
I can't recommend Scratchapixel enough for diving deep into the concepts behind CG (although it seems to be down for me at the moment ironically). I can't remember how much it goes into libraries or if it sticks to implementing things from scratch, but I find knowing the concepts behind something makes learning the libraries much easier anyway.
Syntax-wise, I've found learnxinyminutes.com to be a good introductory resource. I'm also looking for a good quality resource on programmatic conventions for different languages, including details on what unique/'cool' features each has, all in once place. So far I've not had much luck.
I agree with you that people should probably choose a career in something they're good at, but I think that's separate to the issue of making life easier for people entering the subject from nothing. The CS courses I've seen are different from those in other subjects in that they assume a whole lot more background knowledge, which is a pretty exclusionary assumption to make. Stopping this is no bad thing.
Can you clarify what you mean by this please?