Problem in migrating design from Quartus 9.0 (SOPC) to 13.1 (Qsys)

The NIOS2_HAS_DEBUG_STUB define has no effect. It changes the action taken when exception happens, but the exception itself is still there.

The issue seems to be caused by a missing irq handler. The strange thing is that with the debugger I see a valid handler short before the exception happens, then it become NULL when alt_irq_enable() is called. Anyway I don't know if this is simply an artifact, since the code goes through a lot of macros and inlined functions which could mislead the debugger.

Going deeper I found that the exception is thrown when code calls NIOS_WRITE_STATUS(context), where context=1;

I don't know if this is related to my problem, but I get many of these warning messages during project build:

0 [main] pwd 6064 find_fast_cwd: WARNING: Couldn't compute FAST_CWD pointer. Please report this problem to

the public mailing list cygwin@cygwin.com

0 [main] sh 4956 find_fast_cwd: WARNING: Couldn't compute FAST_CWD pointer. Please report this problem to

the public mailing list cygwin@cygwin.com

0 [main] sh 5384 find_fast_cwd: WARNING: Couldn't compute FAST_CWD pointer. Please report this problem to

the public mailing list cygwin@cygwin.com

...