When Design Space Explorer (DSE) 2.0 is run, it archives your project and runs DSE 2.0 off the archive. Due to a problem in the Quartus® II software version 14.1, DSE 2.0 does not automatically pick up all the project files.
To work around this problem, manually archive your project and tell DSE 2.0 to use this archive for its compilation. Here are the steps:
1. Launch Quartus II GUI and create a *.qar archive via menu item Project->Archive Project. Click Advanced settings and select the "Automatically detected source file" option.
2. Open the project in DSE 2.0, in the Archive Settings, select Use existing design archive and set the Quartus II archive (.qar) file name: to the qar file that was previously created.
This problem is fixed beginning with version 15.0 of the Quartus II software.