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Click the project name, right click -> Clean Project to run "make distclean"
Check the console tab for errors. The "Problems" tab isn't very reliable.
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General documentation is at http://help.eclipse.org/luna/index.jsp?topic=%2Forg.eclipse.cdt.doc.user%2Ftasks%2Fcdt_o_run.htm&cp=10_3_5 and http://wiki.eclipse.org/CDT/User/FAQ
For RTEMS specific steps, see this subpage.
A similar page for remote debugging LinuxRT targets is in the works. Some key points:
Where your app is started on the target, command line or startup script, start it with gdbserver. For example, the script could contain the line "/usr/bin/gdbserver :10000 ./bin/evrLab iocStartup.cmd".
When setting up the debug configuration in Eclipse, use the gdb corresponding to the compiler. For example, if your LinuxRT app gets compiled with
/afs/slac/package/linuxRT/buildroot-2014.08/host/linux-x86/usr/bin/i686-linux-g++
then you want to select for your gdb
/afs/slac/package/linuxRT/buildroot-2014.08/host/linux-x86/usr/bin/i686-linux-gdb
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