I have just built a clean git clone of geany and geany-plugins.
./configure --disable-all-plugins --enable-scope

Using Debug | Setup Program dialogue I attempt to set "Working dir" but it will not accept a dir. In fact this seems to be a FILE open dialogue. I have to select file and click "open", then manually edit off the file name part

Fedora 20, using gtk2 2.24.27

I have not worked wiht GTK+ recently but I would have thought there is an option to select a dir instead of a file.

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