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1) Will try that out, once I find the time. Thanks for the answer!
2) I'll experiment on that as well and will report back with how it goes.
3) Nice, awesome!
4) I'd be enough to merely have the works indexed inside Hydrus. You can always CTRL+E to open in your preferred reader/program with all the capabilities you need on the media itself. It's just so you can collect and organize the files, which Hydrus really blows anything else I know out of the water. There's some academic software that lets you organize your sources and stuff, but it's more of a list thing. Since you can add tons of metadata... well let's just say Hydrus and zlib would go hand in hand ;)
5) Yeah, collapsible tag trees would make stuff more easily readable. I know you can organize by custom namespaces and that is already really powerful, but it'd be cool to have tag:one tag:two tag:three below each other in the tag list and in the folder list as well, in "blocks" so to speak.
I feel you on automation. One misstep and you practically DDoS a site or flood your hard drive. I also didn't listen to your warning in the documentation haha. "and then THEY DO SO only to work through thousands of files", I felt that so hard and it brought a smile to my face. But once you have figured out what you want to parse daily etc. you then really want the automation for these specifica.
I really do appreciate your time man. Your project is one I always look into the documentation again and check the forums here. That's a rare exception for a really solid project. If you go the academic/library route, you might catch some licensing stuff to capitalize on your outstanding work, like for official use and stuff.