diff --git a/.gitignore b/.gitignore
index daf0ef997..c0690f1c7 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,24 +1,46 @@
+*.sig
+stamp-*
+
+# Backup files generated by various editors
 *.orig
 *.rej
-*.sig
-*.tar.gz
-*.tar.lz
 *~
-.deps
-.libs
-ABOUT-NLS
-ChangeLog
-Makefile
+
+# 'autoscan' log files
+/autoscan.log
+/configure.scan
+
+# Files generated by Autotools
+/ABOUT-NLS
+/ChangeLog
+/aclocal.m4
+/autom4te.cache/
+/build-aux/
+/configure
+/m4/
 Makefile.in
-aclocal.m4
-autom4te.cache
-autoscan.log
-build-aux/
-config.log
-config.status
-configure
-configure.scan
-flex-*/
-libtool
-m4/
-stamp-*
+
+# Files generated by 'configure'
+/config.cache
+/config.log
+/config.status
+/libtool
+Makefile
+
+# Built object files and support files
+/flex
+/flex.exe
+/libfl.la
+/stage1bin/
+/stage1flex
+/stage1flex.exe
+*.lo
+*.o
+*.obj
+.deps/
+.libs/
+
+# Distribution tarballs and directory
+/flex-*/
+*.tar.gz
+*.tar.lz
diff --git a/Makefile.am b/Makefile.am
index 848f7c8a3..1046b9bc8 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -47,33 +47,37 @@ dist_noinst_SCRIPTS = \
 	po/update_linguas.sh
 
 SUBDIRS = \
-	src \
-	doc \
-	examples \
+	. \
 	po \
-	tests \
-	tools
+	tests
+
+MOSTLYCLEANFILES =
+
+CLEANFILES =
+
+indentfiles =
+
+include doc/local.mk
+include examples/local.mk
+include src/local.mk
+include tools/local.mk
 
 # Convenience targets to build libfl only
 # These are actually wrappers around automake- and libtool-generated targets
 
-libfl:
-	cd src && $(MAKE) $(AM_MAKEFLAGS) libfl.la libfl.pc
+libfl: libfl.la src/libfl.pc
 
 install-libfl:
-	cd src && \
 	$(MAKE) $(AM_MAKEFLAGS) lib_LTLIBRARIES=libfl.la \
-	pkgconfig_DATA=libfl.pc install-libLTLIBRARIES install-pkgconfigDATA
+	pkgconfig_DATA=src/libfl.pc install-libLTLIBRARIES install-pkgconfigDATA
 
 uninstall-libfl:
-	cd src && \
 	$(MAKE) $(AM_MAKEFLAGS) \
-	lib_LTLIBRARIES=libfl.la pkgconfig_DATA=libfl.pc \
+	lib_LTLIBRARIES=libfl.la pkgconfig_DATA=src/libfl.pc \
 	uninstall-libLTLIBRARIES uninstall-pkgconfigDATA
 
 # libfl.pc is cleaned via 'distclean' target
 clean-libfl:
-	cd src && \
 	$(MAKE) $(AM_MAKEFLAGS) lib_LTLIBRARIES=libfl.la clean-libLTLIBRARIES \
 	clean-libtool
 
@@ -84,8 +88,23 @@ ChangeLog: $(srcdir)/tools/git2cl
 		$(srcdir)/tools/git2cl > $@ \
 	; fi
 
-indent:
-	cd src && $(MAKE) $(AM_MAKEFLAGS) indent
+# Run GNU indent on sources. Don't run this unless all the sources compile cleanly.
+#
+# Whole idea:
+#   1. Check for .indent.pro, otherwise indent will use unknown
+#      settings, or worse, the GNU defaults.)
+#   2. Check that this is GNU indent.
+#   3. Make sure to process only the NON-generated .c and .h files.
+#   4. Run indent twice per file. The first time is a test.
+#      Otherwise, indent overwrites your file even if it fails!
+
+indent: .indent.pro
+	for f in $(indentfiles); do \
+		echo indenting $$f; \
+		INDENT_PROFILE=.indent.pro $(INDENT) <$$f >/dev/null && \
+		INDENT_PROFILE=.indent.pro $(INDENT) $$f || \
+		echo $$f FAILED to indent; \
+	done;
 
 install-exec-hook:
 	cd $(DESTDIR)$(bindir) && \
diff --git a/configure.ac b/configure.ac
index e166c8af4..0eeaf38dd 100644
--- a/configure.ac
+++ b/configure.ac
@@ -127,6 +127,10 @@ AC_PATH_PROG([HELP2MAN], help2man, [\${top_srcdir}/build-aux/missing help2man])
     AC_MSG_WARN(help2man: program not found: building man page will not work)
   )
 
+AM_CONDITIONAL([AUTO_BUILD_MAN_PAGE],
+  [test "$HELP2MAN" != "\${top_srcdir}/build-aux/missing help2man" &&
+    { test "x$enable_bootstrap" = xyes || test "$cross_compiling" = no; }])
+
 AC_PATH_PROGS([TEXI2DVI], [gtexi2dvi texi2dvi], [\${top_srcdir}/build-aux/missing texi2dvi])
   AS_IF([test "$TEXI2DVI" = "\${top_srcdir}/build-aux/missing texi2dvi"],
     AC_MSG_WARN(texi2dvi: program not found: building pdf version of manual will not work)
@@ -215,14 +219,8 @@ AS_IF([test "$cross_compiling" = yes],
 
 AC_CONFIG_FILES(
 Makefile
-doc/Makefile
-examples/Makefile
-examples/fastwc/Makefile
-examples/manual/Makefile
 po/Makefile.in
 src/libfl.pc
-src/Makefile
-tools/Makefile
 tests/Makefile
 )
 
diff --git a/doc/.gitignore b/doc/.gitignore
index a685ba6e7..83b010866 100644
--- a/doc/.gitignore
+++ b/doc/.gitignore
@@ -25,6 +25,3 @@ flex.ps
 version.texi
 flex.html
 flex.t2p
-
-flex
-flex.exe
diff --git a/doc/Makefile.am b/doc/Makefile.am
deleted file mode 100755
index a32f81c60..000000000
--- a/doc/Makefile.am
+++ /dev/null
@@ -1,51 +0,0 @@
-if CROSS
-FLEX = $(top_builddir)/src/stage1flex
-else
-FLEX = $(top_builddir)/src/flex$(EXEEXT)
-endif
-
-TEXI2DVI = @TEXI2DVI@ -I $(srcdir)/../examples/manual/
-TEXI2PDF = @TEXI2PDF@ -I $(srcdir)/../examples/manual/
-
-info_TEXINFOS =	flex.texi
-AM_MAKEINFOFLAGS = -I $(srcdir)/../examples/manual/
-dist_man_MANS = flex.1
-MAINTAINERCLEANFILES = flex.1
-
-CLEANFILES = \
-	*.aux \
-	*.cp \
-	*.cps \
-	*.fn \
-	*.fns \
-	*.hk \
-	*.hks \
-	*.ky \
-	*.log \
-	*.op \
-	*.ops\
-	*.pg \
-	*.toc \
-	*.tp \
-	*.tps \
-	*.vr \
-	*.vrs \
-	flex
-
-# Use a fixed program name, without extension (such as ".exe"), for man
-# page generation. 'help2man' strips directory prefix ("./") from the
-# usage string, but not file extensions.
-
-flex.1: $(top_srcdir)/configure.ac $(top_srcdir)/src/cpp-flex.skl $(top_srcdir)/src/options.c $(top_srcdir)/src/options.h
-	( cd $(top_builddir)/src && \
-	  prog_name=`echo '$(FLEX)' | sed 's|^$(top_builddir)/src/||'` && \
-	  $(MAKE) $(AM_MAKEFLAGS) $$prog_name \
-	)
-	$(INSTALL) -m 700 $(FLEX) flex$(EXEEXT)
-	$(HELP2MAN) \
-	--name='$(PACKAGE_NAME)' \
-	--section=1 \
-	--source='The Flex Project' \
-	--manual='Programming' \
-	--output=$@ \
-	./flex
diff --git a/doc/local.mk b/doc/local.mk
new file mode 100644
index 000000000..dedcf6109
--- /dev/null
+++ b/doc/local.mk
@@ -0,0 +1,76 @@
+if CROSS
+FLEX_FOR_DOC = stage1bin/flex
+else
+FLEX_FOR_DOC = flex
+endif
+
+TEXI2DVI = @TEXI2DVI@ -I $(srcdir)/examples/manual/
+TEXI2PDF = @TEXI2PDF@ -I $(srcdir)/examples/manual/
+
+info_TEXINFOS = doc/flex.texi
+AM_MAKEINFOFLAGS = -I $(srcdir)/examples/manual/
+dist_man_MANS = doc/flex.1
+MAINTAINERCLEANFILES = doc/flex.1
+
+CLEANFILES += \
+	doc/*.aux \
+	doc/*.cp \
+	doc/*.cps \
+	doc/*.fn \
+	doc/*.fns \
+	doc/*.hk \
+	doc/*.hks \
+	doc/*.ky \
+	doc/*.log \
+	doc/*.op \
+	doc/*.ops \
+	doc/*.pg \
+	doc/*.toc \
+	doc/*.tp \
+	doc/*.tps \
+	doc/*.vr \
+	doc/*.vrs \
+	doc/flex
+
+# Use a fixed program name, without extension (such as ".exe"), for man
+# page generation. 'help2man' strips directory prefix from the usage
+# string, but not file extensions.
+#
+# Note: Do NOT run the '$(FLEX_FOR_DOC)$(BUILD_EXEEXT)' target in
+# another instance of 'make'! The scanner code also depends on the
+# target and two 'make' instances may contest building the same file.
+
+if AUTO_BUILD_MAN_PAGE
+doc/flex.1: $(FLEX_FOR_DOC)$(BUILD_EXEEXT)
+	$(MKDIR_P) doc
+	$(HELP2MAN) \
+	--name='$(PACKAGE_NAME)' \
+	--section=1 \
+	--source='The Flex Project' \
+	--manual='Programming' \
+	--output=$@ \
+	./$(FLEX_FOR_DOC)
+else
+doc/flex.1: $(srcdir)/configure.ac $(srcdir)/src/cpp-flex.skl $(srcdir)/src/options.c $(srcdir)/src/options.h
+	@option_text=''; \
+	{ test '$(FLEX_FOR_DOC)' = flex || \
+	  : $${option_text=" with --enable-bootstrap'"}; }; \
+	echo "error: flex man page outdated; please install help2man and rerun 'configure'$${option_text}" 1>&2;
+	@false
+endif
+
+distclean-local: distclean-local-doc
+
+# Clean the man page in the build directory only if it is not the
+# source directory.
+
+distclean-local-doc:
+	test '$(srcdir)' = . || { \
+	  if mv -f $(srcdir)/doc/flex.1 $(srcdir)/doc/flex.1.tmp; then \
+	  s=0; else s=$$? || :; fi; \
+	  rm -f doc/flex.1 || :; \
+	  test "$$s" -ne 0 || \
+	    mv -f $(srcdir)/doc/flex.1.tmp $(srcdir)/doc/flex.1; \
+	}
+
+.PHONY: distclean-local-doc
diff --git a/examples/fastwc/Makefile.am b/examples/fastwc/local.mk
similarity index 82%
rename from examples/fastwc/Makefile.am
rename to examples/fastwc/local.mk
index b2831d986..dfc07e442 100644
--- a/examples/fastwc/Makefile.am
+++ b/examples/fastwc/local.mk
@@ -19,11 +19,11 @@
 # WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
 # PURPOSE.
 
-EXTRA_DIST = \
-	wc5.l \
-	wc4.l \
-	wc3.l \
-	wc2.l \
-	wc1.l \
-	mywc.c \
-	README
+EXTRA_DIST += \
+	examples/fastwc/wc5.l \
+	examples/fastwc/wc4.l \
+	examples/fastwc/wc3.l \
+	examples/fastwc/wc2.l \
+	examples/fastwc/wc1.l \
+	examples/fastwc/mywc.c \
+	examples/fastwc/README
diff --git a/examples/Makefile.am b/examples/local.mk
similarity index 86%
rename from examples/Makefile.am
rename to examples/local.mk
index 62688babb..85d7741f7 100644
--- a/examples/Makefile.am
+++ b/examples/local.mk
@@ -19,11 +19,10 @@
 # WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
 # PURPOSE.
 
-EXTRA_DIST = \
-	testxxLexer.l \
-	debflex.awk \
-	README
+EXTRA_DIST += \
+	examples/testxxLexer.l \
+	examples/debflex.awk \
+	examples/README
 
-SUBDIRS = \
-	manual \
-	fastwc
+include examples/fastwc/local.mk
+include examples/manual/local.mk
diff --git a/examples/manual/Makefile.am b/examples/manual/Makefile.am
deleted file mode 100644
index 24affe1b9..000000000
--- a/examples/manual/Makefile.am
+++ /dev/null
@@ -1,58 +0,0 @@
-# This file is part of flex.
-
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions
-# are met:
-
-# 1. Redistributions of source code must retain the above copyright
-#    notice, this list of conditions and the following disclaimer.
-# 2. Redistributions in binary form must reproduce the above copyright
-#    notice, this list of conditions and the following disclaimer in the
-#    documentation and/or other materials provided with the distribution.
-
-# Neither the name of the University nor the names of its contributors
-# may be used to endorse or promote products derived from this software
-# without specific prior written permission.
-
-# THIS SOFTWARE IS PROVIDED ``AS IS'' AND WITHOUT ANY EXPRESS OR
-# IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
-# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
-# PURPOSE.
-
-EXTRA_DIST = \
-	ChangeLog \
-	Makefile.examples \
-	README \
-	cat.lex   \
-	dates.lex \
-	datetest.dat \
-	eof_rules.lex \
-	eof_test01.txt \
-	eof_test02.txt \
-	eof_test03.txt \
-	example_er.lex \
-	example_r.lex \
-	example_nr.lex \
-	expr.lex \
-	expr.y \
-	front.lex \
-	front.y \
-	j2t.lex \
-	myname.lex \
-	myname.txt \
-	myname2.lex \
-	numbers.lex \
-	pas_include.lex \
-	pascal.lex \
-	reject.lex \
-	replace.lex \
-	string1.lex \
-	string2.lex \
-	strtest.dat \
-	unput.lex \
-	user_act.lex \
-	userinit.lex \
-	wc.lex \
-	yymore.lex \
-	yymore2.lex \
-	yymoretest.dat
diff --git a/examples/manual/local.mk b/examples/manual/local.mk
new file mode 100644
index 000000000..726ddac54
--- /dev/null
+++ b/examples/manual/local.mk
@@ -0,0 +1,58 @@
+# This file is part of flex.
+
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions
+# are met:
+
+# 1. Redistributions of source code must retain the above copyright
+#    notice, this list of conditions and the following disclaimer.
+# 2. Redistributions in binary form must reproduce the above copyright
+#    notice, this list of conditions and the following disclaimer in the
+#    documentation and/or other materials provided with the distribution.
+
+# Neither the name of the University nor the names of its contributors
+# may be used to endorse or promote products derived from this software
+# without specific prior written permission.
+
+# THIS SOFTWARE IS PROVIDED ``AS IS'' AND WITHOUT ANY EXPRESS OR
+# IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+# PURPOSE.
+
+EXTRA_DIST += \
+	examples/manual/ChangeLog \
+	examples/manual/Makefile.examples \
+	examples/manual/README \
+	examples/manual/cat.lex \
+	examples/manual/dates.lex \
+	examples/manual/datetest.dat \
+	examples/manual/eof_rules.lex \
+	examples/manual/eof_test01.txt \
+	examples/manual/eof_test02.txt \
+	examples/manual/eof_test03.txt \
+	examples/manual/example_er.lex \
+	examples/manual/example_r.lex \
+	examples/manual/example_nr.lex \
+	examples/manual/expr.lex \
+	examples/manual/expr.y \
+	examples/manual/front.lex \
+	examples/manual/front.y \
+	examples/manual/j2t.lex \
+	examples/manual/myname.lex \
+	examples/manual/myname.txt \
+	examples/manual/myname2.lex \
+	examples/manual/numbers.lex \
+	examples/manual/pas_include.lex \
+	examples/manual/pascal.lex \
+	examples/manual/reject.lex \
+	examples/manual/replace.lex \
+	examples/manual/string1.lex \
+	examples/manual/string2.lex \
+	examples/manual/strtest.dat \
+	examples/manual/unput.lex \
+	examples/manual/user_act.lex \
+	examples/manual/userinit.lex \
+	examples/manual/wc.lex \
+	examples/manual/yymore.lex \
+	examples/manual/yymore2.lex \
+	examples/manual/yymoretest.dat
diff --git a/po/.gitignore b/po/.gitignore
index 3c6f57d67..c3e4c382f 100644
--- a/po/.gitignore
+++ b/po/.gitignore
@@ -1,18 +1,26 @@
-*.gmo
-Makefile
-Makefile.in
-Makefile.in.in
-Makevars.template
-POTFILES
-Rules-quot
-boldquot.sed
-en@boldquot.*header
 en@boldquot.po
-en@quot.*header
 en@quot.po
-flex.pot
-insert-header.sin
-quot.sed
-remove-potcdate.sed
-remove-potcdate.sin
 stamp-*
+
+# Files generated by Autotools
+/Makefile.in.in
+/Makevars.template
+/Rules-quot
+/boldquot.sed
+/en@boldquot.header
+/en@quot.header
+/insert-header.sin
+/quot.sed
+/remove-potcdate.sin
+
+# Files generated by 'configure'
+/Makefile
+/Makefile.in
+/POTFILES
+
+# Built object files and support files
+/*.gmo
+/en@boldquot.insert-header
+/en@quot.insert-header
+/flex.pot
+/remove-potcdate.sed
diff --git a/src/.gitignore b/src/.gitignore
index cbae2e3b6..d5ae0af23 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -1,21 +1,18 @@
-*.la
-*.lo
-*.o
-*-flex.h
-config.h
-config.h.in
-config_for_build.h
-flex
-libfl.pc
-parse.c
-parse.h
-scan.c
-stage1scan.c
-stage1flex
-stage2compare
-stage2scan.c
+# Files generated by Autotools
+/config.h.in
 
-# for MSWindows
+# Files generated by 'configure'
+/config.h
+/config_for_build.h
+/libfl.pc
 
-*.obj
-*.exe
+# Generated code, included in distribution tarball only
+/parse.c
+/parse.h
+/scan.c
+
+# Built object files and support files
+/*-flex.h
+/stage1scan.c
+/stage2compare
+/stage2scan.c
diff --git a/src/Makefile.am b/src/Makefile.am
deleted file mode 100644
index b9ead0740..000000000
--- a/src/Makefile.am
+++ /dev/null
@@ -1,231 +0,0 @@
-AM_YFLAGS = -d
-AM_CPPFLAGS = -DLOCALEDIR=\"$(localedir)\"
-AM_CFLAGS = $(WARNINGFLAGS)
-LIBS = @LIBS@
-pkgconfigdir = @pkgconfigdir@
-
-m4 = @M4@
-
-bin_PROGRAMS = flex
-if ENABLE_BOOTSTRAP
-noinst_PROGRAMS = stage1flex
-if !CROSS
-noinst_DATA = stage2compare
-endif
-endif
-
-if ENABLE_LIBFL
-lib_LTLIBRARIES = libfl.la
-pkgconfig_DATA = libfl.pc
-endif
-libfl_la_SOURCES = \
-	libmain.c \
-	libyywrap.c
-libfl_la_LDFLAGS = -version-info @SHARED_VERSION_INFO@
-
-stage1flex_SOURCES = \
-	scan.l \
-	$(COMMON_SOURCES)
-
-nodist_stage1flex_SOURCES = \
-	$(SKELINCLUDES)
-
-if CROSS
-stage1flex_LDADD =
-stage1flex_SOURCES += \
-		      ../lib/malloc.c \
-		      ../lib/realloc.c
-stage1flex_LINK = $(LIBTOOL) --tag=CC --mode=link $(CC_FOR_BUILD) \
-		  $(CFLAGS_FOR_BUILD) $(LDFLAGS_FOR_BUILD) -o $@
-
-$(stage1flex_OBJECTS): CC=$(CC_FOR_BUILD)
-$(stage1flex_OBJECTS): CFLAGS=$(CFLAGS_FOR_BUILD) -DUSE_CONFIG_FOR_BUILD
-$(stage1flex_OBJECTS): CPP=$(CPP_FOR_BUILD)
-$(stage1flex_OBJECTS): CPPFLAGS=$(CPPFLAGS_FOR_BUILD)
-$(stage1flex_OBJECTS): LDFLAGS=$(LDFLAGS_FOR_BUILD)
-else
-stage1flex_LDADD = $(LDADD)
-stage1flex_LINK = $(LINK)
-stage1flex_CFLAGS = $(AM_CFLAGS)
-endif
-
-flex_SOURCES = \
-	$(COMMON_SOURCES)
-
-nodist_flex_SOURCES = \
-	$(SKELINCLUDES)
-
-if ENABLE_BOOTSTRAP
-nodist_flex_SOURCES += stage1scan.c
-else
-flex_SOURCES += scan.l
-endif
-
-COMMON_SOURCES = \
-	buf.c \
-	ccl.c \
-	dfa.c \
-	ecs.c \
-	filter.c \
-	flexdef.h \
-	flexint.h \
-	flexint_shared.h \
-	gen.c \
-	main.c \
-	misc.c \
-	nfa.c \
-	options.c \
-	options.h \
-	parse.y \
-	regex.c \
-	scanflags.c \
-	scanopt.c \
-	scanopt.h \
-	skeletons.c \
-	sym.c \
-	tables.c \
-	tables.h \
-	tables_shared.c \
-	tables_shared.h \
-	tblcmp.c \
-	version.h \
-	yylex.c
-
-LDADD = $(LIBOBJS) @LIBINTL@
-
-$(LIBOBJS): $(LIBOBJDIR)$(am__dirstamp)
-
-include_HEADERS = \
-	FlexLexer.h
-
-EXTRA_DIST = \
-	c99-flex.skl \
-	cpp-flex.skl \
-	go-flex.skl \
-	mkskel.sh \
-	gettext.h \
-	chkskel.sh
-
-MOSTLYCLEANFILES = \
-	$(SKELINCLUDES) \
-	stage1scan.c \
-	stage2scan.c \
-	stage2compare
-
-CLEANFILES = stage1flex$(EXEEXT)
-
-SKELINCLUDES = \
-	cpp-flex.h \
-	c99-flex.h \
-	go-flex.h
-
-cpp-flex.h: cpp-flex.skl mkskel.sh flexint_shared.h tables_shared.h tables_shared.c
-	$(SHELL) $(srcdir)/mkskel.sh cpp $(srcdir) $(m4) $(VERSION) > $@.tmp
-	$(SHELL) $(srcdir)/chkskel.sh $@.tmp
-	mv -f $@.tmp $@
-
-c99-flex.h: c99-flex.skl mkskel.sh
-	$(SHELL) $(srcdir)/mkskel.sh c99 $(srcdir) $(m4) $(VERSION) > $@.tmp
-	$(SHELL) $(srcdir)/chkskel.sh $@.tmp
-	mv -f $@.tmp $@
-
-go-flex.h: go-flex.skl mkskel.sh
-	$(SHELL) $(srcdir)/mkskel.sh go $(srcdir) $(m4) $(VERSION) > $@.tmp
-	$(SHELL) $(srcdir)/chkskel.sh $@.tmp
-	mv -f $@.tmp $@
-
-# The input and output file names are fixed for deterministic scanner
-# generation. If scan.l is not modified by builders, stage1scan.c should
-# be bit-identical to the scan.c pregenerated on release.
-stage1scan.c: scan.l stage1flex$(EXEEXT)
-	( cd $(srcdir) && $(abs_builddir)/stage1flex$(EXEEXT) \
-	  $(AM_LFLAGS) $(LFLAGS) -o scan.c -t scan.l ) >$@ || \
-	{ s=$$?; rm -f $@; exit $$s; }
-
-# Unlike stage1scan.c, we leave stage2scan.c intact when the generation
-# fails. This allow users to examine generation errors.
-stage2scan.c: scan.l flex$(EXEEXT) stage1scan.c
-	( cd $(srcdir) && $(abs_builddir)/flex$(EXEEXT) \
-	  $(AM_LFLAGS) $(LFLAGS) -o scan.c -t scan.l ) >$@
-
-stage2compare: stage1scan.c
-	@rm -f stage2scan.c; \
-	$(MAKE) $(AM_MAKEFLAGS) stage2scan.c; \
-	echo Comparing stage1scan.c and stage2scan.c; \
-	cmp stage1scan.c stage2scan.c || { \
-	  s=$$?; \
-	  echo "Bootstrap comparison failure!"; \
-	  exit $$s; \
-	}; \
-	echo Comparison successful.; \
-	echo success >$@
-
-dist-hook: scan.l flex$(EXEEXT)
-	chmod u+w $(distdir) && \
-	chmod u+w $(distdir)/scan.c && \
-	( cd $(srcdir) && $(abs_builddir)/flex$(EXEEXT) \
-	  -o scan.c -t scan.l ) >scan.c && \
-	mv -f scan.c $(distdir)
-
-# make needs to be told to make inclusions so that parallelized runs will
-# not fail.
-
-stage1flex-skeletons.$(OBJEXT): $(SKELINCLUDES)
-skeletons.$(OBJEXT): $(SKELINCLUDES)
-
-stage1flex-main.$(OBJEXT): parse.h
-main.$(OBJEXT): parse.h
-
-stage1flex-yylex.$(OBJEXT): parse.h
-yylex.$(OBJEXT): parse.h
-
-stage1flex-scan.$(OBJEXT): parse.h
-stage1scan.$(OBJEXT): parse.h
-scan.$(OBJEXT): parse.h
-
-# Run GNU indent on sources. Don't run this unless all the sources compile cleanly.
-#
-# Whole idea:
-#   1. Check for .indent.pro, otherwise indent will use unknown
-#      settings, or worse, the GNU defaults.)
-#   2. Check that this is GNU indent.
-#   3. Make sure to process only the NON-generated .c and .h files.
-#   4. Run indent twice per file. The first time is a test.
-#      Otherwise, indent overwrites your file even if it fails!
-indentfiles = \
-	buf.c \
-	ccl.c \
-	dfa.c \
-	ecs.c \
-	scanflags.c \
-	filter.c \
-	flexdef.h \
-	gen.c \
-	libmain.c \
-	libyywrap.c \
-	main.c \
-	misc.c \
-	nfa.c \
-	options.c \
-	options.h \
-	regex.c \
-	scanopt.c \
-	scanopt.h \
-	sym.c \
-	tables.c \
-	tables.h \
-	tables_shared.c \
-	tables_shared.h \
-	tblcmp.c
-
-indent: $(top_srcdir)/.indent.pro
-	cd $(top_srcdir) && \
-	for f in $(indentfiles); do \
-		f=src/$$f; \
-		echo indenting $$f; \
-		INDENT_PROFILE=.indent.pro $(INDENT) <$$f >/dev/null && \
-		INDENT_PROFILE=.indent.pro $(INDENT) $$f || \
-		echo $$f FAILED to indent; \
-	done;
-
-.PHONY: indent
diff --git a/src/local.mk b/src/local.mk
new file mode 100644
index 000000000..51ff3d78c
--- /dev/null
+++ b/src/local.mk
@@ -0,0 +1,264 @@
+AM_YFLAGS = -d
+AM_CPPFLAGS = -I$(srcdir)/src -DLOCALEDIR=\"$(localedir)\"
+AM_CFLAGS = $(WARNINGFLAGS)
+LIBS = @LIBS@
+pkgconfigdir = @pkgconfigdir@
+
+m4 = @M4@
+
+bin_PROGRAMS = flex
+
+EXTRA_PROGRAMS = stage1flex
+if ENABLE_BOOTSTRAP
+if !CROSS
+noinst_DATA = src/stage2compare
+endif
+endif
+
+if ENABLE_LIBFL
+lib_LTLIBRARIES = libfl.la
+pkgconfig_DATA = src/libfl.pc
+endif
+libfl_la_SOURCES = \
+	src/libmain.c \
+	src/libyywrap.c
+libfl_la_LDFLAGS = -version-info @SHARED_VERSION_INFO@
+
+stage1flex_SOURCES = \
+	src/scan.l \
+	$(COMMON_SOURCES)
+
+nodist_stage1flex_SOURCES = \
+	$(SKELINCLUDES)
+
+if CROSS
+
+stage1flex_SOURCES += \
+	lib/malloc.c \
+	lib/realloc.c
+
+stage1flex_CPPFLAGS = -DUSE_CONFIG_FOR_BUILD $(AM_CPPFLAGS)
+
+# This also overrides AM_LIBTOOLFLAGS and AM_LDFLAGS
+stage1flex_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(LIBTOOLFLAGS) \
+	--mode=link $(CC_FOR_BUILD) $(CFLAGS_FOR_BUILD) \
+	$(LDFLAGS_FOR_BUILD) -o $@
+
+stage1flex_LDADD =
+
+else
+
+stage1flex_CPPFLAGS = $(AM_CPPFLAGS)
+
+stage1flex_LINK = $(LIBTOOL) $(AM_V_lt) --tag=CC $(LIBTOOLFLAGS) \
+	--mode=link $(CCLD) $(CFLAGS) $(LDFLAGS) -o $@
+
+stage1flex_LDADD = $(LDADD)
+
+endif
+
+# Suppress build warnings when compiling and linking stage1flex.
+stage1flex_CFLAGS =
+
+# Override the 'stage1flex$(EXEEXT)' target automake would generate.
+# If the compiler is not $(CC_FOR_BUILD) when this target is invoked,
+# delete the object files that would be linked to 'stage1flex' to force
+# rebuild all of them.
+
+stage1flex$(EXEEXT): $(stage1flex_OBJECTS) $(stage1flex_DEPENDENCIES) $(EXTRA_stage1flex_DEPENDENCIES)
+	@rm -f stage1flex$(EXEEXT)
+	{ test 'x$(CC)' = 'x$(CC_FOR_BUILD)' && \
+	  test 'x$(CPP)' = 'x$(CPP_FOR_BUILD)'; } || \
+	  { rm -f src/stage1flex-*.$(OBJEXT) \
+	    src/$(DEPDIR)/stage1flex-*.Po || :; }
+	@{ test 'x$(CC)' = 'x$(CC_FOR_BUILD)' && test 'x$(CPP)' = 'x$(CPP_FOR_BUILD)'; } || { \
+	  echo 'error: stage1flex must be built with a native compiler' 1>&2; \
+	  exit 1; \
+	}
+	$(AM_V_CCLD)$(stage1flex_LINK) $(stage1flex_OBJECTS) $(stage1flex_LDADD) $(LIBS)
+
+# The 'stage1bin/flex$(BUILD_EXEEXT)' target is not managed by
+# automake. We use a different file name from the automake-managed
+# 'stage1flex$(EXEEXT)' target to avoid clashing.
+
+stage1bin/flex$(BUILD_EXEEXT):
+	@if test 'x$(EXEEXT)' != 'x$(BUILD_EXEEXT)'; then rm -f stage1flex$(EXEEXT); else :; fi
+	@if test 'x$(OBJEXT)' != 'x$(BUILD_OBJEXT)'; then rm -f src/stage1flex-*.$(OBJEXT); else :; fi
+	$(MAKE) $(AM_MAKEFLAGS) \
+	  CC='$(CC_FOR_BUILD)' \
+	  CPP='$(CPP_FOR_BUILD)' \
+	  CFLAGS='$(CFLAGS_FOR_BUILD)' \
+	  CPPFLAGS='$(CPPFLAGS_FOR_BUILD)' \
+	  LDFLAGS='$(LDFLAGS_FOR_BUILD)' \
+	  EXEEXT='$(BUILD_EXEEXT)' \
+	  OBJEXT='$(BUILD_OBJEXT)' \
+	  stage1flex$(BUILD_EXEEXT)
+	$(MKDIR_P) stage1bin
+	$(INSTALL) -m 700 stage1flex$(BUILD_EXEEXT) $@
+
+flex_SOURCES = \
+	$(COMMON_SOURCES)
+
+nodist_flex_SOURCES = \
+	$(SKELINCLUDES)
+
+if ENABLE_BOOTSTRAP
+nodist_flex_SOURCES += src/stage1scan.c
+else
+flex_SOURCES += src/scan.l
+endif
+
+COMMON_SOURCES = \
+	src/buf.c \
+	src/ccl.c \
+	src/dfa.c \
+	src/ecs.c \
+	src/filter.c \
+	src/flexdef.h \
+	src/flexint.h \
+	src/flexint_shared.h \
+	src/gen.c \
+	src/main.c \
+	src/misc.c \
+	src/nfa.c \
+	src/options.c \
+	src/options.h \
+	src/parse.y \
+	src/regex.c \
+	src/scanflags.c \
+	src/scanopt.c \
+	src/scanopt.h \
+	src/skeletons.c \
+	src/sym.c \
+	src/tables.c \
+	src/tables.h \
+	src/tables_shared.c \
+	src/tables_shared.h \
+	src/tblcmp.c \
+	src/version.h \
+	src/yylex.c
+
+LDADD = $(LIBOBJS) @LIBINTL@
+
+$(LIBOBJS): $(LIBOBJDIR)$(am__dirstamp)
+
+include_HEADERS = \
+	src/FlexLexer.h
+
+EXTRA_DIST += \
+	src/c99-flex.skl \
+	src/cpp-flex.skl \
+	src/go-flex.skl \
+	src/mkskel.sh \
+	src/gettext.h \
+	src/chkskel.sh
+
+MOSTLYCLEANFILES += \
+	$(SKELINCLUDES) \
+	src/stage1flex-*.$(BUILD_OBJEXT) \
+	src/stage1scan.c \
+	src/stage2scan.c \
+	src/stage2compare
+
+CLEANFILES += \
+	stage1bin/flex$(BUILD_EXEEXT) \
+	stage1flex$(BUILD_EXEEXT) \
+	stage1flex$(EXEEXT)
+
+SKELINCLUDES = \
+	src/cpp-flex.h \
+	src/c99-flex.h \
+	src/go-flex.h
+
+src/cpp-flex.h: src/cpp-flex.skl src/mkskel.sh src/flexint_shared.h src/tables_shared.h src/tables_shared.c
+	$(SHELL) $(srcdir)/src/mkskel.sh cpp $(srcdir)/src $(m4) $(VERSION) > $@.tmp
+	$(SHELL) $(srcdir)/src/chkskel.sh $@.tmp
+	mv -f $@.tmp $@
+
+src/c99-flex.h: src/c99-flex.skl src/mkskel.sh
+	$(SHELL) $(srcdir)/src/mkskel.sh c99 $(srcdir)/src $(m4) $(VERSION) > $@.tmp
+	$(SHELL) $(srcdir)/src/chkskel.sh $@.tmp
+	mv -f $@.tmp $@
+
+src/go-flex.h: src/go-flex.skl src/mkskel.sh
+	$(SHELL) $(srcdir)/src/mkskel.sh go $(srcdir)/src $(m4) $(VERSION) > $@.tmp
+	$(SHELL) $(srcdir)/src/chkskel.sh $@.tmp
+	mv -f $@.tmp $@
+
+# The input and output file names are fixed for deterministic scanner
+# generation. If scan.l is not modified by builders, stage1scan.c should
+# be bit-identical to the scan.c pregenerated on release.
+src/stage1scan.c: src/scan.l stage1bin/flex$(BUILD_EXEEXT)
+	( cd $(srcdir)/src && $(abs_builddir)/stage1bin/flex$(BUILD_EXEEXT) \
+	  $(AM_LFLAGS) $(LFLAGS) -o scan.c -t scan.l ) >$@ || \
+	{ s=$$?; rm -f $@; exit $$s; }
+
+# Unlike stage1scan.c, we leave stage2scan.c intact when the generation
+# fails. This allow users to examine generation errors.
+src/stage2scan.c: src/scan.l flex$(EXEEXT)
+	( cd $(srcdir)/src && $(abs_builddir)/flex$(EXEEXT) \
+	  $(AM_LFLAGS) $(LFLAGS) -o scan.c -t scan.l ) >$@
+
+
+src/stage2compare: src/stage1scan.c src/stage2scan.c
+	@echo Comparing stage1scan.c and stage2scan.c; \
+	cmp src/stage1scan.c src/stage2scan.c || { \
+	  s=$$?; \
+	  echo "Bootstrap comparison failure!"; \
+	  exit $$s; \
+	}; \
+	echo Comparison successful.; \
+	echo success >$@
+
+dist-hook: dist-hook-src
+
+dist-hook-src: src/scan.l flex$(EXEEXT)
+	chmod u+w $(distdir)/src && \
+	chmod u+w $(distdir)/src/scan.c && \
+	( cd $(srcdir)/src && $(abs_builddir)/flex$(EXEEXT) \
+	  -o scan.c -t scan.l ) >src/scan.c && \
+	mv -f src/scan.c $(distdir)/src/scan.c
+
+# make needs to be told to make inclusions so that parallelized runs will
+# not fail.
+
+src/stage1flex-skeletons.$(OBJEXT): $(SKELINCLUDES)
+src/skeletons.$(OBJEXT): $(SKELINCLUDES)
+
+src/stage1flex-main.$(OBJEXT): src/parse.h
+src/main.$(OBJEXT): src/parse.h
+
+src/stage1flex-yylex.$(OBJEXT): src/parse.h
+src/yylex.$(OBJEXT): src/parse.h
+
+src/stage1flex-scan.$(OBJEXT): src/parse.h
+src/stage1scan.$(OBJEXT): src/parse.h
+src/scan.$(OBJEXT): src/parse.h
+
+indentfiles += \
+	src/buf.c \
+	src/ccl.c \
+	src/dfa.c \
+	src/ecs.c \
+	src/scanflags.c \
+	src/filter.c \
+	src/flexdef.h \
+	src/gen.c \
+	src/libmain.c \
+	src/libyywrap.c \
+	src/main.c \
+	src/misc.c \
+	src/nfa.c \
+	src/options.c \
+	src/options.h \
+	src/regex.c \
+	src/scanopt.c \
+	src/scanopt.h \
+	src/sym.c \
+	src/tables.c \
+	src/tables.h \
+	src/tables_shared.c \
+	src/tables_shared.h \
+	src/tblcmp.c
+
+.PHONY: dist-hook-src src/stage2scan.c
diff --git a/tests/Makefile.am b/tests/Makefile.am
index fd94e67d4..7d9e55f0f 100644
--- a/tests/Makefile.am
+++ b/tests/Makefile.am
@@ -320,7 +320,7 @@ pthread_pthread_LDADD = @LIBPTHREAD@
 
 TESTOPTS = -L
 
-FLEX = $(top_builddir)/src/flex
+FLEX = $(top_builddir)/flex
 
 .l.c: $(FLEX)
 	$(AM_V_LEX)$(FLEX) $(TESTOPTS) -o $@ $<
diff --git a/tools/Makefile.am b/tools/Makefile.am
deleted file mode 100644
index 46743a669..000000000
--- a/tools/Makefile.am
+++ /dev/null
@@ -1,2 +0,0 @@
-EXTRA_DIST = \
-	git2cl
diff --git a/tools/local.mk b/tools/local.mk
new file mode 100644
index 000000000..f8b15be32
--- /dev/null
+++ b/tools/local.mk
@@ -0,0 +1,2 @@
+EXTRA_DIST += \
+	tools/git2cl