Critical Issue
If you launch the Nios II Software Build Tool for Eclipse from the Nios II command shell, you cannot pause execution of the Nios II application when debugging the application. Running the program in this way closes the GDB connection to the target, leaving the processor running. This is caused by running Eclipse from the Cygwin environment.
To ensure that the pause button works, launch the Nios II Software Build Tool for Eclipse either from Qsys or directly from your operating system\'s Start menu. To launch the Nios II Software Build Tool for Eclipse from Qsys, in the Tools menu, click Nios II Software Build Tools for Eclipse.