The jtag debugger is not working yet. So we will have to use printk to debug kernel. There is a gdbserver binary for userspace at nios2-linux/toolchain-mmu/nios2-linux/bin. (we will add the gdbserver source to uclinux-dist later) You may copy it to romfs/bin. To enable solib in gdb, you will need to run this command or add it to .gdbinit,
set solib-absolute-prefix ~/nios2-linux/toolchain-mmu/x86-linux2/nios2-wrs-linux-gnu/libc
Please refer to the wiki about user space debugging,
DebugApps debug user space applications using gdb, gdbtui, insight or ddd.
EclipseCDT install and develop/debug with Eclipse CDT IDE.