This fixes up makefiles so they work in the Chrome OS build
environment. In particular:
1. Add $(CPPFLAGS) to compiler invocations.
2. Replace bare ar invocation with $(AR) for cross compilation.
3. Add additional flags to silence warnings generated by clang.

--- a/Common/ConsoleIO/makefile
+++ b/Common/ConsoleIO/makefile
@@ -38,10 +38,10 @@
 all: libconsoleio.a
 
 $(OBJFILES): %.o: %.c
-	$(CC) -c $(CFLAGS) $(FPACK) $(INCLUDES) $< -o $@
+	$(CC) -c $(CPPFLAGS) $(CFLAGS) $(FPACK) $(INCLUDES) $< -o $@
 
 libconsoleio.a: $(OBJFILES)
-	ar $(ARFLAGS) $@ $^
+	$(AR) $(ARFLAGS) $@ $^
 
 clean:
 	rm -rfv *.o libconsoleio.a
--- a/Common/Crypt/makefile
+++ b/Common/Crypt/makefile
@@ -38,10 +38,10 @@
 all: libcrypt.a
 
 $(OBJFILES): %.o: %.c
-	$(CC) -c $(CFLAGS) $(FPACK) $(INCLUDES) $< -o $@
+	$(CC) -c $(CPPFLAGS) $(CFLAGS) $(FPACK) $(INCLUDES) $< -o $@
 
 libcrypt.a: $(OBJFILES)
-	ar $(ARFLAGS) $@ $^
+	$(AR) $(ARFLAGS) $@ $^
 
 clean:
 	rm -rfv *.o libcrypt.a
--- a/Common/FileIO/makefile
+++ b/Common/FileIO/makefile
@@ -37,10 +37,10 @@
 all: libfileio.a
 
 $(OBJFILES): %.o: %.c
-	$(CC) -c $(CFLAGS) $(FPACK) $(INCLUDES) $< -o $@
+	$(CC) -c $(CPPFLAGS) $(CFLAGS) $(FPACK) $(INCLUDES) $< -o $@
 
 libfileio.a: $(OBJFILES)
-	ar $(ARFLAGS) $@ $^
+	$(AR) $(ARFLAGS) $@ $^
 
 clean:
 	rm -rfv *.o libfileio.a
--- a/Common/MicroTss/makefile
+++ b/Common/MicroTss/makefile
@@ -69,10 +69,10 @@
 all: libmicrotss.a
 
 $(OBJFILES): %.o: %.c
-	$(CC) -c $(CFLAGS) $(FPACK) $(INCLUDES) $< -o $@
+	$(CC) -c $(CPPFLAGS) $(CFLAGS) $(FPACK) $(INCLUDES) $< -o $@
 
 libmicrotss.a: $(OBJFILES)
-	ar $(ARFLAGS) $@ $^
+	$(AR) $(ARFLAGS) $@ $^
 
 clean:
 	rm -rfv *.o libmicrotss.a
--- a/Common/Platform/makefile
+++ b/Common/Platform/makefile
@@ -36,10 +36,10 @@
 all: libplatform.a
 
 $(OBJFILES): %.o: %.c
-	$(CC) -c $(CFLAGS) $(FPACK) $(INCLUDES) $< -o $@
+	$(CC) -c $(CPPFLAGS) $(CFLAGS) $(FPACK) $(INCLUDES) $< -o $@
 
 libplatform.a: $(OBJFILES)
-	ar $(ARFLAGS) $@ $^
+	$(AR) $(ARFLAGS) $@ $^
 
 clean:
 	rm -rfv *.o libplatform.a
--- a/Common/TpmDeviceAccess/makefile
+++ b/Common/TpmDeviceAccess/makefile
@@ -40,10 +40,10 @@
 all: libtpmdeviceaccess.a
 
 $(OBJFILES): %.o: %.c
-	$(CC) -c $(CFLAGS) $(FPACK) $(INCLUDES) $< -o $@
+	$(CC) -c $(CPPFLAGS) $(CFLAGS) $(FPACK) $(INCLUDES) $< -o $@
 
 libtpmdeviceaccess.a: $(OBJFILES)
-	ar $(ARFLAGS) $@ $^
+	$(AR) $(ARFLAGS) $@ $^
 
 clean:
 	rm -rfv *.o libtpmdeviceaccess.a
--- a/TPMFactoryUpd/makefile
+++ b/TPMFactoryUpd/makefile
@@ -13,7 +13,6 @@
 #
 # The makefile uses the gcc compiler.
 #
-STRIP=strip --strip-unneeded $@  # Don't strip if you want to debug
 #FPACK+= -fpack-struct # Don't pack structs globally. This would crash OpenSSL decrypt operation
 
 # Basic compiler options
@@ -29,13 +28,17 @@
 	-Wunreachable-code \
 	-DLINUX
 
-CC = gcc
+# Additional flags to make the source compile with clang.
+CFLAGS+= \
+	-Wno-newline-eof \
+	-Wno-gnu-zero-variadic-macro-arguments \
+	-Wno-cast-align
 
 # Export compiler flags to sub-makefiles
 export CFLAGS
 export CC
 
-LDFLAGS=\
+LDFLAGS+=\
 	-lcrypt -L../Common/Crypt \
 	-lplatform -L../Common/Platform \
 	-lmicrotss -L../Common/MicroTss \
@@ -103,7 +106,7 @@
 coverage: TPMFactoryUpd
 
 $(OBJFILES): %.o: %.c
-	$(CC) -c $(CFLAGS) $(FPACK) $(INCLUDES) $< -o $@
+	$(CC) -c $(CPPFLAGS) $(CFLAGS) $(FPACK) $(INCLUDES) $< -o $@
 
 TPMFactoryUpd: $(OBJFILES)
 	# Call shared sub-makefiles to generate archives
@@ -114,7 +117,7 @@
 	$(MAKE) -C ../Common/TpmDeviceAccess
 	$(MAKE) -C ../Common/Crypt
 	# And run the actual makefile job
-	$(CC) $^ -o $@ $(LDFLAGS)
+	$(CC) $^ -o $@ $(CFLAGS) $(LDFLAGS)
 	$(STRIP)
 
 clean: