Use "Store project file inside the project base directory" by default
Personally I usually do this anyway, what do other people think?
I've been keeping project files together, outside of the project folders. To switch to something else, I can double click the relevant project file without having to do much navigation in the file manager. To access the contents of the project folder with the file manager or terminal, I use a keybinding with geany/geany-plugins#1126.
geany/geany.geany
geany/geany-plugins.geany
geany/plugin-geanylua.geany
geany/plugin-project-organizer.geany
geany/plugin-tweaks-ui.geany
geany/plugin-etc.geany
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