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I've found this, but there is someting in that code that disgust me. Dunno why and don't get me wrong - it looks like working solution, but when I use an external plugin, I don't want to edit/modify it - and here I would have to - for example because 'bookmark' file location is hardcoded (this might be my weird ocd-like rules speaking), so I'm looking for alternatives.
Take a look at z.lua. Might be what you're looking for.
Looks like https://github.com/baskerville/fdb will suit you. It stores the paths in binary format, hence it's compact and fast. There are commands to add, remove and query a path. The documentation is scarce, but it's not that hard to figire out how to use. It's written in Rust, but the API makes it suitable for any shell, just wrap it as you like.
Or wd ?