JabRef is a desktop application for managing BibTeX and BibLaTeX libraries. Prior to 6.0-alpha.6, when jabsrv or JabRef's built-in HTTP server is enabled, the GET /better-bibtex/cayw endpoint accepts an external command query parameter and CAYWQueryParams.getCommand() passes it through CAYWResource.getCitation() into PushToSublimeText.getCommandLine(). On Unix-like systems, PushToSublimeText combines this untrusted cite-command prefix and citation keys into a string executed through sh -c by ProcessBuilder without shell escaping. A client that can cause a localhost request with application=sublime can inject shell metacharacters and execute operating-system commands as the JabRef user when a valid Sublime Text command path is configured and the victim completes the CAYW selection dialog. The built-in server is disabled by default, so exploitation requires the victim to enable it or run jabsrv. This issue is fixed in version 6.0-alpha.6.

JabRef version <=4.3.1 contains a XML External Entity (XXE) vulnerability in MsBibImporter XML Parser that can result in disclosure of confidential data, denial of service, server side request forgery, port scanning. This attack appear to be exploitable via Specially crafted MsBib file. This vulnerability appears to have been fixed in after commit 89f855d.