Zotero
Drop-in replacementFree with paid extrasThe same program from the same makers. Sign in and your library is there. Plugs into LibreOffice Writer for citations.
Your files: Your whole library syncs from your account. Nothing needs exporting.
Verdict: Yes
Yes. Zotero publishes an official Linux version, and your library, folders and notes sync down from your account exactly as they are on Windows.
Zotero's download page offers Linux alongside Windows and Mac, in 64-bit, ARM and 32-bit forms. This is the same program made by the same nonprofit, not a community port.
Installing it is the only slightly fiddly part. The official download is a file you unpack and run from a folder, and Zotero also recommends a maintained package for Ubuntu and Debian users that handles updates through the normal app store machinery. There is a Flathub listing too, which is the easiest route for most people, although that one is packaged by volunteers rather than by Zotero.
After that, sign in and everything appears. References, folders, tags, notes and attached PDFs all come down from your account. Remember to add the Zotero Connector to Firefox or Chrome, because that is the button that saves a paper into your library from a web page.
The word processor plugin works too. Zotero hooks into LibreOffice Writer on Linux the way it hooks into Word on Windows, so citations and bibliographies keep updating themselves. Documents you already wrote in Word keep their citation fields when opened in LibreOffice, though it is worth checking a copy before trusting a thesis to it.
The same program from the same makers. Sign in and your library is there. Plugs into LibreOffice Writer for citations.
Your files: Your whole library syncs from your account. Nothing needs exporting.
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