Which of my project files should I be 'adding' (recursively)?
All files you are interested in. It does not matter
Or in other words, why is this question even asked and what is the outcome of it?
If you are using the makefile project it absolutely makes not difference.... All files are ignored by codeblocks and only the Makefile counts
Should this be with a make clean or make distclean, first, or not, or does it matter?
Not sure what you mean here, but if you call Build->Clean with a makefile project codeblocks calls the command line
If you use a Makefile project, codeblocks is only a better text editor. The build system is completely circumvented (This means settings of Project->Build options, or files in the Project are ignored by codeblocks. Only things in the Makefile count).
It doesn't seem to be putting this project in gnote.cbp, because if I start over it still knows about it, and asks me if I want to overwrite it. For later backup purposes where is this project being saved to?
I am not quite sure what you mean... but the project is stored in
Resulting filename: /home/howard/src/gnote/gnote-3.30.0/gnote/gnote.cbp
It would probably better if you alter this path in the "new project" dialog to
/home/howard/src/gnote/gnote-3.30.0/gnote.cbp
or simply copy the existing project file to
/home/howard/src/gnote/gnote-3.30.0/gnote.cbp
Codeblocks does not care about absolute paths... Maybe you have to fix your Makefile path if you move the project file