I have been desperately trying to import a multimodule maven project from GIT into my (freshly installed) STS 3.9.4. During the last hours I tried lots of solutions that were posted on stack overflow, but none of them worked for me.
These are the steps I did:
git cloned the repo from the command line (intentionally, because it didn't work either when I used the GIT integration of STS)- imported the project via
File/Import/Maven/Existing Maven Projects
After the project was imported, it looks like this:

(please ignore the red icon at the top left, the problems persists even when this icon is not there)
I can Run As / Maven Install any pom.xml, but when I try to edit java sourcecode Eclipse tells me The resource is not on the build path of a Java project.
To fix this I tried:
- convert to faceted form
- added Java nature
Configure Build Path/Set as source folder- add
buildcommandorg.eclipse.jdt.core.javabuilderto .project
Being able to build is fine, but editing sourcecode without support for Organize Imports, Format Source, and so on is a real pain.
The solution to this problem was somehow hidden, but in the end I have to say the reason was clear. After I checked with a different multimodule project (https://github.com/Activiti/Activiti.git), I was sure that my STS and other components don't suffer from a generic problem. So the cause must be located in the project itself.
The multimodule project was setup correctly on the
pom.xmllevel. But the topmostpom.xmlwas modified: most of the modules had been commented out:The developer who introduced that change didn't experience any problems because he kept his already existing workspace. And the problem only occurs when a new workspace gets created and maven scans the pom files.