Okay, so I made a mistake of setting my home directory (~, a.k.a. /home/user) to be my workspace location on my RHEL6 box.
I want to change my workspace to ~/workspace.
I was testing to move files manually from workspace and suddenly my eclipse did not show them in my eclipse view so i moved them back to the same location where they have come from, entered eclipse and clicked right click on the package where i am expecting those files and clicked Refresh, Now i can view them on my Eclipse under packages, so try do refreshing it might work for u.