I've got a partial patch:

diff --git a/ghc.mk b/ghc.mk
index eedb023..37ef2f2 100644
--- a/ghc.mk
+++ b/ghc.mk
@@ -719,7 +719,7 @@ ifneq "$(BINDIST)" "YES"
 
 ifneq "$(BOOTSTRAPPING_CONF)" ""
 ifeq "$(wildcard $(BOOTSTRAPPING_CONF))" ""
-$(shell echo "[]" >$(BOOTSTRAPPING_CONF))
+$(shell $(GHC_PKG) init $(BOOTSTRAPPING_CONF))
 endif
 endif
 

But I'm dying here:

===--- building phase 1
make -r --no-print-directory -f ghc.mk phase=1 phase_1_builds
libraries/hpc/ghc.mk:3: libraries/hpc/dist-boot/build/.depend-v.haskell: No such file or directory
compiler/ghc.mk:646: compiler/stage1/build/.depend-v.haskell: No such file or directory
ghc/ghc.mk:114: ghc/stage1/build/.depend.haskell: No such file or directory
"rm" -f ghc/stage1/build/.depend.haskell.tmp  
"/home/hs01/ezyang/ghc-head/inplace/bin/ghc-stage2" -M -static  -H32m -O  -package-db libraries/bootstrapping.conf  -hide-all-packages -i -ighc/. -ighc/stage1/build -ighc/stage1/build/autogen -Ighc/stage1/build -Ighc/stage1/build/autogen     -optP-include -optPghc/stage1/build/autogen/cabal_macros.h -package-key array_GX4NwjS8xZkC2ZPtjgwhnz -package-key base_ESD4aQEEWwsHtYJVc1BwtJ -package-key bytes_Kc0PyaputnzDnBdZW0y2Gv -package-key direc_1OR7Bu5EIqqJUPTpfzOCIt -package-key filep_34DFDFT9FVD9pRLLgh8IdQ -package-key ghc_GE0xPzNsQzT2p10hpwDwSW -package-key proce_JJ2k66FcGHSLNmYZUkX8Td -package-key unix_4dEexQFispVG782agZacZC -Wall -XHaskell2010   -no-user-package-db -rtsopts      -odir ghc/stage1/build -hidir ghc/stage1/build -stubdir ghc/stage1/build -dep-makefile ghc/stage1/build/.depend.haskell.tmp -dep-suffix "" -include-pkg-deps  ghc/./Main.hs
<command line>: cannot satisfy -package-key ghc_GE0xPzNsQzT2p10hpwDwSW
    (use -v for more information)
ghc/ghc.mk:114: recipe for target 'ghc/stage1/build/.depend.haskell' failed
make[1]: *** [ghc/stage1/build/.depend.haskell] Error 1
Makefile:71: recipe for target 'all' failed
make: *** [all] Error 2

A bit hard to diagnose due to #9651 (closed). Recording this so I don't forget.