iBooks management of PDF files

I’ve always used “Open in iBooks” to view PDF files I come across on the internet. I don’t do anything explicit to save these files, but it seems something does because when I open iBooks, those PDFs are all there. I have hundreds of these PDFs, but iBooks doesn’t seem to support folders to organize the files. The first problem is that I can’t seem to get an app like PDF Pro to see the PDFs that I viewed in iBooks.

Does iOS save these PDF files, and where are they save?

Using Collections is inadequate for my needs. Does iBooks support nested folders? How would one create the folder structure, and populate it with the PDFs?

Usually the .pdf files can be only viewed in Safari without opening in iBooks, and this is as such since I remember, and this is default in any browser.

To save them, you have the option to "open in iBooks" and they will copied there, and the different Collection items is the only possibility to categorise them in iBooks.

But in Safari there are another possibility: from sharing symbol, choose "Save to Files" - and there you may create any number of folders, nested or not, as you wish/need.

The good news is you can move those .pdf files from iBooks: go Library -> Collections -> Edit and select the files you intend to move to Files and again, from sharing symbol choose "Save to Files" - then delete them from iBooks.