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What exactly is your use-case? To save the file so all the on_save changes (tabs, trailing spaces, newlines, plugin changes) and conversions (BOM, encoding) get done or to save the buffer which is just writing the bytes somewhere to be reloaded later, somewhat like a bulk undo.
The former needs to be done in Geany, and because the whole file writing thing is messy and convoluted would probably (from only limited evaluation) be a fair bit of work.
The latter (and the reload) could easily be done in a plugin, if there is enough demand maybe even the core saveactions plugin.
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