The Markdown plugin just feeds formatted strings to WebKit view, it never writes any files to the file system, so Refresh from WebKit's point of view doesn't make much sense here. Markdown [uses `file://.`](https://github.com/geany/geany-plugins/blob/master/markdown/src/viewer.c#L35...) for the base URI, it might work somehow if a valid base URI was used, like the real URI of the uncompiled markdown text file or something.
It might also be possible to hook into WebKit's Refresh command and make it just re-update with a formatted string like it normally does. If anyone wants to implement that, I'd review it.
@belkka is your use-case that you've updated the file outside of Geany? If so, maybe you could use <kbd>Ctrl</kbd>+<kbd>R</kbd> to reload the document in Geany (it will be nagging you anyway), this should re-update the WebKit view.
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