but it doesn't mention the GTK version it was built with.

Menu->Help->Debug Messages near the top, tells you the version its actually using.

Does Geany retain its speed with GTK3 ?

Million line files are not really in Geany's main use-case which is human edited files. It only takes a few tens of thousands of lines before the liveware fails. 😁

Even so scrolling of a few million lines shouldn't be a problem after all the loading and analysis is finished. Do you have wrap lines on? That tends to be slow due to all the analysis needed by Scintilla to decide the wrap, that depends more on the Pango version than GTK.

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