An example of .project contains
<linkedResources>
    <link>
        <name>node_lib</name>
        <type>2</type>
        <location>E:/Nodejs/node-v0.10.22/node-v0.10.22/lib</location>
    </link>
</linkedResources>
How to add linked resources programmatically?
org.eclipse.core.resources.IProjectDescription does not have related methods

So this Q mentions getLinks() for IProject  (JavaDoc has no)
Eclipse Add marker for linked resources
Related to:
Programmatically remove linked files from the project in eclipse
UPDATED: Solved with help of both answers, as they brought understanding of Eclipse terminology (what is what)
Code
   IFolder link = project.getFolder("Link");
   IPath location = new Path("TEMP/folder");
   if (workspace.validateLinkLocation(location).isOK()) {
      link.createLink(location, IResource.NONE, null);
   } else {
      //invalid location, throw an exception or warn user
   }
 
     
     
    