Selfhosted
A place to share alternatives to popular online services that can be self-hosted without giving up privacy or locking you into a service you don't control.
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bookshelf looks like something you'd like. It doesn't seem to automatically index the files, but it does work without Calibre and has no UI. It only supports Epub though.
I don't know if it saves progress and I can't test it right now.
It doesn't support OPDS-PSE, which is the most common way of tracking progress.