Quite a lot to get through here, let's see if I can answer all your questions properly
First of all, thanks for considering my problem in such depth. I wasn't aware that it may take a lot of work to make it easier to delete books & their associated folders on the kindle itself. I don't mean to sound demanding at all. I kinda just wanted to see if anybody else would also like this feature, and maybe they'd fix it and then I'd be eternally grateful
Yes, I tried kindle explorer. There was no "checkbox" system, or similar, in which I could select a whole bunch of files/directories and delete them all in one go. To delete files in kindle explorer you have to select each one individually and click the delete button, after which is a prompt asking to confirm deletion. That's clunky and time consuming. Not to mention the fact that you have to delete the book, and also the folder containing that weird extra information related to the book. So kindle explorer isn't an apt solution to this problem - deleting files is just as time consuming as on the normal firmware.
Yes, I absolutely would love something that would easily allow deletion of sets
of files - books, related indexes and folders. I can live with deleting each book individually, with the following conditions:
1.) You don't have to confirm deletion
2.) entire sets of files are deleted relating to the deleted book
Midnight Commander for kindle looks like it would be difficult to install (requiring more than simply copying a folder into my extensions folder) - so please don't think me rude if I don't install it and check it out. From what I can see, it's simply another file explorer. It won't provide the ability to delete sets of files when a book is deleted. Deleting a book and its related folders is even clunky in windows explorer. I can't imagine any kindle file manager/explorer being better than windows explorer - which is already bad enough!
I hadn't realised before that the kindle does not delete those folders when you delete a book.
Now, I just tried folder pruner, and as you say it deletes some things but not others. I was still left with some folders belonging to books that don't exist any more.
I have no idea whether books are saved on the cloud properly or not, or which ones are saved to the cloud. Sorry :/ It sounds like all those extra files do is store bookmarks and last reading position (and maybe notes, which I never use). If I'm deleting a book, there's no way I want to keep all that stuff as well. So I'd be happy with a solution which nukes everything related to a deleted book.
Doing all this on Calibre would be a pain, to be honest. I like to leave my computer out of it when doing things on the kindle. Most of what I read on the kindle is articles I've pushed from the web (not using the official kindle extension for chrome - I use a different one) and those articles never see calibre in .mobi form. After I read them, I delete them on the device. But those extra files and folders remain, making a real mess of the documents folder if I need to delete several books within windows explorer. That only happens when I have a backlog of articles stored on the kindle. Rather than spend time holding down my finger on each one, selecting delete, and confirming the delete, you'd think deleting batches of files in windows explorer would be easier - but the mess of files & folders makes that almost as difficult :/
I hope all this helps you make better sense of what I would like. If I'm alone in finding this to be a problem, don't worry about it. I really would hate to waste anybody's time.
Do ask me to clarify things further, if needed!