Why do I need to do a quartus_cdb --merge

I use a Makefile to do my fpga build, which cycles through quartus_map, quartus_fit, quartus_asm, and quartus_sta. All was working fine until I called up the GUI version 10.1. The Makefile is run on version 7.2 (I know it is old).

Now it fails fitter right at the start saying I need to run "quartus_cdb --merge <design>". It is merging my "top" design and "sld_hub:sld_bug_inst" which is an Encrypted Megafunction. This as been there before and I never had to run merge before.

How do I make the fitter do the merge without my intervention like it was doing before?