CDT will build too much by default with the "all" target, so you need to tweak it.
Right click the project directory and choose "Build Configurations" and then "Manage...":
Then delete the "Debug" build and rename the "Release" build to "Default" and give it a description:
Now right click the project directory and select properties at the bottom:
First un-check "Generate Makefiles automatically", then correct the build directory to "${workspace_loc:/freeems-vanilla/src}":
Then correct the build target by changing it from "all" to "s19":
At this point you should be able to right click the project directory or enter the Project menu and choose "Build Project". In the lower panel is a tab called "Console" which should end in the sequence "**** Build Finished ****", congratulations, you just built the firmware in Eclipse! :-)
Fred.