I started a brand new project in CDT where I was using MOOS and I could not get my simple program to link. While everything looked fine on the surface I just could not get the IDE to link to the MOOS libraries. I know the OS and MOOS itself was not a problem as I had other projects in the same workspace which did link correctly. The only difference between those and this was that I setup this project from scratch, whilst the others I had not. It took me a while to figure it out, but in the end I had to resort to explicitly add the locations for the libs in the C++ project properties in CDT as shown in the screenshot below.
To get this this, you right click on the Project name in Project Explorer in CDT. In the C++ Linker section then explicitly add the two paths shown in the screenshot. I of course had MOOS installed in the default location (binaries are in /usr/local/bin and libraries in /usr/local/lib). So even if you have added paths to CDT and still getting linking issues, I suggest you add it explicitly to the C++ properties.
