What you are trying to do, and how you are wanting to do it, is
unclear to me (I can be a bit thick :().
It
seems like you are wanting to formulate a query, that will be processed by an unmentioned utility, on an unknown platform, to parse DokuWiki pages of unknown content (and using unknown plugins), to be used in a DokuWiki.
If you could clarify the objectives, workflow, tools, and the OS in use it would be easier for readers to provide an answer. Update what?, use GitHub how? (Jekyll, Gollum?).
Perhaps if you could include an example case?
Notes: there
are a number of DokuWiki users that have taken large amounts of files in one format, and automated the process of converting those files into DokuWiki content, likewise changing existing DokuWiki files based on known criteria - and they have used a number of different methods to do so; on a Linux/Unix system searching existing DokuWiki files for certain tags (find/grep "regex"), and changing those files (awk/sed) is a fairly simple task, depending on your existing experience (searching 1600 files for matches takes only a couple of minutes on a low-powered computer) - so knowing your OS makes a difference to suggested methods.