If you want to set up your Contiki development environment on a server rather than using the Instant Contiki virtual machine, this is for you.
Follow the steps in Contiki wiki page .
Instead of cloning the Contiki repo in the Step 3 mentioned above, you should upload the Contiki folder from the Instant Contiki VM to your server. This is because the repo is outdated somehow. I had the problem that the source file cannot be compiled using the source files in