Your problem is that when you run make a non-virgin source pull you need to specify REGENIE=1 to recalculate the makefiles. (Doing so takes a while, which is why you don't want to specify that once you've locked in an agreeable built/test/repeat cycle).
make (whatever) REGENIE=1 TOOLS=1 builds the tools.
A side note: the Ensoniq drivers got updated in .171 (the LCD emulation and front panel emulation was much improved for the SQ-1 and SQ-R, among other things) so if you plan to work on the SD-1 and friends it's advisable to work off of at least .171 and ideally a fresh pull from Github.
