The linking functionality has changed in Project Server 2013, in Project Server 2010 you used to create the links on the Custom Commands tab as shown below:
In 2013 this feature has been updated and no longer exists on the new or edit forms. This blog post covers how you can links items in 2013 using the web interface.
Firstly we will look at how you do this from one of the lists, in this example we will use the Issues list. As you can see in the image below, I have 2 issues:
To link Issue 1 to a task in the project, click Issue 1 and you will see the following page:
Click Add Related Item:
Double click Tasks:
Select the task required and click Insert:
Issue 1 will now show task T1 as the related item:
Clicking T1 will load the display form for T1 and show Issue 1 as the related item:
The project schedule in PWA will show the Issue icon that links to the Issue (same as 2010):
It is the same process described above to link Issues to Risks or Risks to Issues etc.
The second method to link tasks to issues is from the Tasks list on the project site:
Click one of the tasks:
Click Show More:
Click Add Related Item and follow the same steps above to select the related item.
The third method is from the schedule page in PWA. Select the task from the grid and click the Options tab:
Click the Related Items button on the ribbon and that task will open from the task list on the project site:
Notice this time the Related Items is displaying by default. This is due to &ShowRelatedItems=1 being appended to the URL. Now follow the same steps detailed above to select the related item.
Slightly more steps to link items but very simple.