They are in the same folder. I believe I have that issue resolved since it has started building again.
I did also have run configurations setup to use dfu-util to flash firmware to the module. However now I get this error:
dfu-util: Could not open file core-firmware.bin for reading: No such file or directory
It seems the binary file is either not being generated or being placed in the wrong directory. Where are these settings set in Eclipse?
Perhaps I spoke too soon. I am still getting the same error. Here is a screen shot of my Eclipse workspace. You can see that all required repositories are in the workspace. Is there some way I have to link them in Eclipse?
Thank you very much for the help @mdma. I did finally resolve my problem. I had inadvertently moved the core-common-lib folder at some point and that was the main cause of the problem. Once I got all three back in the same root directory everything is building and flashing through dfu-util in eclipse now. I have no idea how that folder got moved.