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The warnings are a result of packages exporting a non-existing paths in their manifest, see these previous discussions on ros-users:
http://ros-users.122217.n3.nabble.com/ROS-Eclipse-warnings-td2479833.html
http://ros-users.122217.n3.nabble.com/Please-remove-references-to-msg-cpp-and-srv-cpp-from-package-manifests-td2168967.html#a2170278
Packages still exporting these paths should be ticketed for a fix (they just need to remove the non-existant include path from the manifest). That being said, I don't think it's related to your first problem. I have seen plently of these warnings using Eclipse, but never your first error.
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