@elextr following your suggestion, it is working now. As you mentioned, GDB doesn't find the files, even after they are added to the search path with dir, until after the program starts running. But they're available after (gdb) start so that's fine.

Seems like this should be added to the documentation. Maybe something like

Because most of Geany is a library, in order to use GDB, you'll need to install the version of Geany you want to debug. You can install to a different directory in order to not overwrite an existing install with ./configure --prefix <a directory>. You'll also need to tell GDB about where the source files are with GDB's dir command. Most source files won't be loaded until after Geany starts running, but you can run (gdb) start to break at the start of main and set breakpoints etc. from there.

in the GDB section of HACKING?

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