diff --git a/Makefile b/Makefile
index f205e546..706e7eed 100644
--- a/Makefile
+++ b/Makefile
@@ -82,7 +82,6 @@ bootstrap: icyc
 	cp scheme/cyclone/cgen.c $(BOOTSTRAP_DIR)/scheme/cyclone
 	cp scheme/cyclone/util.c $(BOOTSTRAP_DIR)/scheme/cyclone
 	cp cyclone.c $(BOOTSTRAP_DIR)/cyclone.c
-	cp Makefile.bootstrap $(BOOTSTRAP_DIR)/Makefile
 	cp Makefile.config $(BOOTSTRAP_DIR)/Makefile.config
 
 
diff --git a/Makefile.bootstrap b/Makefile.bootstrap
deleted file mode 100644
index 00e71251..00000000
--- a/Makefile.bootstrap
+++ /dev/null
@@ -1,92 +0,0 @@
-# Cyclone Scheme
-# Copyright (c) 2014, Justin Ethier
-# All rights reserved.
-#
-# Makefile for bootstrapping cyclone from generated C files.
-
-include Makefile.config
-
-CFLAGS = -g
-LIBS = -lcyclone -lm
-
-COBJ = scheme/base scheme/read scheme/write scheme/char scheme/eval scheme/file scheme/cyclone/common scheme/cyclone/libraries scheme/cyclone/transforms scheme/cyclone/cgen scheme/cyclone/util
-CFILES = $(addsuffix .c, $(COBJ))
-COBJECTS=$(CFILES:.c=.o)
-
-%.o: %.c %.h
-	$(CC) $(CFLAGS) $< -c -o $@
-
-all: cyclone icyc unit-tests
-
-libcyclone.a: runtime.c include/cyclone/runtime.h dispatch.c
-	$(CC) -g -c -Iinclude dispatch.c -o dispatch.o
-	$(CC) -g -c -Iinclude -DCYC_INSTALL_DIR=\"$(PREFIX)\" -DCYC_INSTALL_LIB=\"$(LIBDIR)\" -DCYC_INSTALL_INC=\"$(INCDIR)\" -DCYC_INSTALL_SLD=\"$(DATADIR)\" runtime.c -o runtime.o
-	$(AR) rcs libcyclone.a runtime.o dispatch.o
-
-cyclone: $(COBJECTS) libcyclone.a
-	$(CC) cyclone.c $(CFLAGS) -c -o cyclone.o
-	$(CC) cyclone.o $(COBJECTS) $(LIBS) $(CFLAGS) -o cyclone
-
-icyc: cyclone
-	./cyclone icyc.scm
-
-unit-tests: unit-tests.scm
-	cyclone unit-tests.scm && ./unit-tests
-
-.PHONY: clean
-clean:
-	rm -rf *.o *.a *.so cyclone icyc unit-tests test.out test.txt scheme/*.o scheme/cyclone/*.o icyc.c unit-tests.c
-
-# Install dependencies required to actually build this project
-install-deps:
-	$(MKDIR) $(DESTDIR)$(LIBDIR)
-	$(MKDIR) $(DESTDIR)$(INCDIR)
-	$(MKDIR) $(DESTDIR)$(DATADIR)
-	$(MKDIR) $(DESTDIR)$(DATADIR)/scheme/cyclone
-	$(INSTALL) -m0644 include/cyclone/*.h $(DESTDIR)$(INCDIR)/
-	$(INSTALL) -m0644 scheme/*.scm $(DESTDIR)$(DATADIR)/scheme
-	$(INSTALL) -m0644 scheme/*.sld $(DESTDIR)$(DATADIR)/scheme
-	$(INSTALL) -m0644 scheme/cyclone/*.scm $(DESTDIR)$(DATADIR)/scheme/cyclone
-	$(INSTALL) -m0644 scheme/cyclone/*.sld $(DESTDIR)$(DATADIR)/scheme/cyclone
-
-install-libs:
-	$(MKDIR) $(DESTDIR)$(LIBDIR)
-	$(INSTALL) -m0644 libcyclone.a $(DESTDIR)$(LIBDIR)/
-
-install-cyclone:
-	$(MKDIR) $(DESTDIR)$(DATADIR)/scheme/cyclone
-	$(INSTALL) -m0755 cyclone $(DESTDIR)$(BINDIR)/
-	$(INSTALL) -m0644 scheme/*.o $(DESTDIR)$(DATADIR)/scheme
-	$(INSTALL) -m0644 scheme/cyclone/*.o $(DESTDIR)$(DATADIR)/scheme/cyclone
-
-# Install everything. Can not call this directly initially as 
-# dependencies are required by portions of the build.
-install:
-	$(MKDIR) $(DESTDIR)$(BINDIR)
-	$(MKDIR) $(DESTDIR)$(LIBDIR)
-	$(MKDIR) $(DESTDIR)$(INCDIR)
-	$(MKDIR) $(DESTDIR)$(DATADIR)
-	$(MKDIR) $(DESTDIR)$(DATADIR)/scheme/cyclone
-	$(INSTALL) -m0755 cyclone $(DESTDIR)$(BINDIR)/
-	$(INSTALL) -m0755 icyc $(DESTDIR)$(BINDIR)/
-	$(INSTALL) -m0644 libcyclone.a $(DESTDIR)$(LIBDIR)/
-	$(INSTALL) -m0644 include/cyclone/*.h $(DESTDIR)$(INCDIR)/
-	$(INSTALL) -m0644 scheme/*.scm $(DESTDIR)$(DATADIR)/scheme
-	$(INSTALL) -m0644 scheme/*.sld $(DESTDIR)$(DATADIR)/scheme
-	$(INSTALL) -m0644 scheme/*.o $(DESTDIR)$(DATADIR)/scheme
-	$(INSTALL) -m0644 scheme/cyclone/*.scm $(DESTDIR)$(DATADIR)/scheme/cyclone
-	$(INSTALL) -m0644 scheme/cyclone/*.sld $(DESTDIR)$(DATADIR)/scheme/cyclone
-	$(INSTALL) -m0644 scheme/cyclone/*.o $(DESTDIR)$(DATADIR)/scheme/cyclone
-
-uninstall:
-	$(RM) $(DESTDIR)$(BINDIR)/cyclone
-	$(RM) $(DESTDIR)$(BINDIR)/icyc
-	$(RM) $(DESTDIR)$(LIBDIR)/libcyclone.a
-	$(RM) $(DESTDIR)$(INCDIR)/*.*
-	$(RMDIR) $(DESTDIR)$(INCDIR)
-	$(RM) $(DESTDIR)$(DATADIR)/scheme/cyclone/*.*
-	$(RMDIR) $(DESTDIR)$(DATADIR)/scheme/cyclone
-	$(RM) $(DESTDIR)$(DATADIR)/scheme/*.*
-	$(RMDIR) $(DESTDIR)$(DATADIR)/scheme
-	$(RMDIR) $(DESTDIR)$(DATADIR)
-