I have set up an eclipse workspace. Inside this workspace i have a dynamic web app cloned from repository. My working directory looks like following.

I am seeing a different hierarchy in Eclipse project explorer. My project explorer looks like following.

Ideally it should show src, WebContent, build.xml etc. inside java resources but it shows entire project folder inside java resources.
Troubleshooting I tried: 1. Delete existing project from project explorer and import the project again. 2. Pull the changes in local copy and refresh the project from project explorer. 3. Change the working directory and import a new project.
None of this seemed to resolve the problem.
Appreciate if someone could help me with the root cause and a solution to this.