My first approach was changing the selection settings in filetypes.common, but this did not have any effect.
This should work - it worked for me in the example above and it should override the theme's selection color. So my guess is that there's some syntax error in your `filetypes.common` and as a result of it the file isn't read.
I'd suggest that you try the following: 1. Close Geany 2. `mv ~/.config/geany/filedefs/filetypes.common ~/.config/geany/filedefs/filetypes.common.backup` (i.e. remove your `filetypes.common` and save it under a different filename as a backup) 3. Open Geany, open Tools->Configuration Files->filetypes.common - this should open the Geany's default version of the file 4. Place `selection=000;#F00;false;true` under the `[styling]` section