probably you're missing some files - see iotdk-ide for Linux not working in Ubuntu 14 and the additional tarball provided there: https://software.intel.com/sites/default/files/managed/c0/bb/usr_include_1.tgz
Turns out my installation has those files. However, it made me think perhaps instead of pointing eclipse at /usr/bin/gdb I should be pointing at /opt/poky-edison/1.6.1/sysroots/core2-32-poky-linux/usr/bin/gdb.
When I point at the gdb in the edison sysroots, I also get a failure on gdb --version but the error (seen from both eclipse and at the command line) is as follows:
/opt/poky-edison/1.6.1/sysroots/core2-32-poky-linux/usr/bin/gdb: error while loading shared libraries: libreadline.so.6: cannot open shared object file: No such file or directory
I'm no Eclipse expert, but I ran into similar issues when I was first configuring for remote debugging on the Edison. I couldn't get it working until I modified the Debug Configuration in Eclipse to explicitly point to the i586-poky-linux-gdb debugger.
Hope that helps,
Thanks Aenimated! setting the GDB Debugger: field to i586-poky-linux-gdb did the trick!