I hate to spend time trying to remember things that I already did in the past, but all times that I didn’t document it I always spend time figuring it out.
When compiling an ELF binary in the Atmel ASF studio I need to disable GCC optimization in order to get all debug info from GDB.
To disable Toolchain optimization in the ASF:
Project -> YourProjectName Properties... -> Toolchain -> ARM/GNU C Compiler -> Optimization -> Optimization Level = None (-O0)