To run the contiki examples using Eclipse I always use the following steps and work perfectly:
File --> import --> C/C++ --> Existing Code as Makefile Project -->Next
--> Browse -->choose the folder of the example you want to run (see,the folder of the example containing the .c and Makefile files not the .c file only)(e.g. contiki/examples/hello world)
also, highlight the "Linux GCC" from 'Toolchain for Indexer Setting' menu --> Finish
For Building: right click on the project -->Build Project -->Build All.
To run the example, just click run as usual.
Some unresolved inclusion errors in .c file of the project will be highlighted, so, we need to tell the Eclipse where are the contiki files.
(Also the next steps will enable you to open the headers, functions, variables ..etc declarations of .c files in your project)
Firstly, make another copy of contiki folder (e.g. contiki-Declaration) to be used for this purpose.
right click on the imported project --> New --> folder --> Advance--> Link to alternative location (Linked Folder)--> Browse --> choose "contiki-Declaration" -->Finish
After this, All the errors will be left from your project. Also now you can open the declaration of any contiki function or variable in your project
I hope this help.