I use various pieces of calibre, and appreciate that they can be called from the command line, but don't really use the full application.
I prefer to manually manage my books on Google Drive. I create folders on Google Drive based on topic (Programming/C++, Programming/Python, etc, Musc/Guitar, Music/Piano, etc..., SciFi, etc...) and keep them there. I never keep more than 2 or 3 books on my devices at a time, the one I'm reading and a few extras in case I finish one while away from home.
I wrote a script that uses ebook-convert to download the news recipes that I want, then kepubify (an unrelated tool) to convert them to kepub. It then waits for me to plug in my device and copies them over, deleting any that are > 3 days old. (It can also work with a `-k` switch (for -kindle) to download in mobi format)
I use ebook-convert to convert from various source formats to my desired target format (I have both a Kindle and a Kobo).
I call directly to ebook-viewer to check the conversion output and quality.
I'd like to be able to use a particular plugin from the command line to liberate my books, but with the latest version thy got rid of the standalone command line tool.
The only time I really use the full GUI is if I want to download new covers and update them using the polish tool. I've not figured out how to do that from the command line. Which reminds me, WHY do so many books download with a boring cover after showing you the nice cover on the purchase page? That said, I didn't really care about covers too much because I tend to use list view on my devices, though with the Kobo showing the covers when sleeping I suddenly care a lot more.
Maybe I should just set my Kobo to use custom images that have my contact info instead -- that's how I got my Kindle 3 and favorite backpack back after leaving it on the train years ago.
EDIT: Looks like I can use "ebook-meta --cover" or "ebook-polish -c <image>" for my cover changing needs! Yay