Turns out, the original TiddlyWiki used a java jar to handle the file persistence. (I remember it being so magically automatic, but recently investigated how it was done)

I don't think that's right - IIRC it used to be possible to write out a file, if loaded from a file:// URL, directly from JavaScript. Then that ability got nobbled because security (justifiable) without properly thinking through a good alternative (not justifiable). I mourn the loss of the ability, TiddlyWiki was in a class of its own and there should have been many more systems inspired by its design. Alas.

ETA: Wikipedia has reminded me the feature was called UniversalXPConnect, and it was a Firefox thing and wasn't cross-browser. It still sucks that it was removed without sensible replacement.

I used TiddlyWiki a lot to manage my D&D 3.5 campaign back in the day. As I recall, it originally was a true stand-alone HTML document capable of overwriting itself, but once browsers dropped support for this capability, users had to begin using various workarounds, and this remains the status quo today.

TiddlySaver.jar was one such workaround. A check in the Wayback Machine suggests that it was originally required only for Safari, Opera, and Chrome; IE and Firefox needed no such plugin. Nowadays, there are several workarounds, and setting up one is a mandatory installation step: standalone applications, browser extensions, servers, etc. Some are clunky (e.g. you have to keep your wiki in your Downloads directory or the browser can't write to it), and either way, TiddlyWiki is no longer truly a single stand-alone HTML file, at least not for writing purposes. It's still a very versatile tool, though.