Revert "Moved Makefile.in under template"

This reverts commits:
* 6f9d5fafe0
* bb3c89b643

And remove the dependency of Makefile on Makefile.in
transitionally.

.travis.yml

@@ -370,7 +370,7 @@ before_script:
   - ln -s ~/.downloaded-cache
   - "> config.status"
   - "> .rbconfig.time"
-  - sed -f tool/prereq.status template/Makefile.in common.mk > Makefile
+  - sed -f tool/prereq.status Makefile.in common.mk > Makefile
   - make touch-unicode-files
   - make -s $JOBS $UPDATE_UNICODE up
   - make -s $JOBS srcs

Makefile.in

@@ -334,7 +334,7 @@ install-cross: $(arch)-fake.rb $(RBCONFIG) rbconfig.rb $(arch_hdrdir)/ruby/confi
 	$(INSTALL_DATA) $(LIBRUBY) $(LIBRUBY_A) $(XRUBY_RUBYLIBDIR)/$(arch)
 	$(INSTALL_PROGRAM) $(LIBRUBY_SO) $(XRUBY_RUBYLIBDIR)/$(arch)
 
-Makefile:	$(srcdir)/template/Makefile.in $(srcdir)/enc/Makefile.in
+Makefile:	$(srcdir)/Makefile.in $(srcdir)/enc/Makefile.in
 
 $(MKFILES): config.status $(srcdir)/version.h
 		@[ -f $@ ] && mv $@ $@.old

configure.ac

@@ -3915,7 +3915,7 @@ AS_CASE([" $CPP "], [*" $CC "*], [CPP=`echo " $CPP " | sed "s| $CC |"' $(CC) |;s
 AS_IF([test x"$firstmf" != x], [
     AC_CONFIG_FILES($firstmf:$firsttmpl, [], [firstmf="$firstmf" firsttmpl="$firsttmpl"])
 ])
-AC_CONFIG_FILES(Makefile:template/Makefile.in, [
+AC_CONFIG_FILES(Makefile, [
     tmpmk=confmk$$.tmp
     {
 	AS_IF([test ${VCS+set}], [

defs/gmake.mk

@@ -150,7 +150,7 @@ commit: $(if $(filter commit,$(MAKECMDGOALS)),$(filter-out commit,$(MAKECMDGOALS
 	+$(Q) \
 	{ \
 	  $(CHDIR) "$(srcdir)"; \
-	  sed 's/^@.*@$$//;s/@[A-Za-z_][A-Za-z_0-9]*@//g;/^all-incs:/d' defs/gmake.mk template/Makefile.in; \
+	  sed 's/^@.*@$$//;s/@[A-Za-z_][A-Za-z_0-9]*@//g;/^all-incs:/d' defs/gmake.mk Makefile.in; \
 	  sed 's/{[.;]*$$([a-zA-Z0-9_]*)}//g' common.mk; \
 	} | \
 	$(MAKE) $(mflags) Q=$(Q) ECHO=$(ECHO) srcdir="$(srcdir)" srcs_vpath="" CHDIR="$(CHDIR)" \

tool/make-snapshot

@@ -389,8 +389,7 @@ def package(vcs, rev, destdir, tmp = nil)
       File.open("#{defaults}/ruby.rb", "w") {}
       miniruby = ENV['MINIRUBY'] + " -I. -I#{extout} -rcross"
       baseruby = ENV["BASERUBY"]
-      mk = (IO.read("template/Makefile.in") rescue IO.read("Makefile.in")).
-             gsub(/^@.*\n/, '')
+      mk = IO.read("Makefile.in").gsub(/^@.*\n/, '')
       vars = {
         "EXTOUT"=>extout,
         "PATH_SEPARATOR"=>File::PATH_SEPARATOR,