diff --git a/.gitignore b/.gitignore
index 64217e167..1a868b218 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,94 +1,37 @@
-*.DS_Store
-*.Plo
-*.aux
-*.bbl
-*.blg
-*.brf
-*.d
-*.g6
-*.gz
-*.html
-*.idx
-*.ilg
-*.ind
-*.la
-*.la
-*.lab
-*.lab
-*.lo
-*.log
-*.orig
-*.out
-*.pdf
-*.pnr
-*.pyc
-*.pyc
-*.semigroups
-*.six
-*.swo
-*.swp
-*.synctex.gz
-*.tex
-*.toc
-*.top
-*.tui
-*.txt
-.dirstamp
-.libs
-/libsemigroups/
-Makefile
-/Makefile.in
-Transitions*
-_*.xml
-_AutoDocMainFile.xml
-_Chunks.xml
-aclocal.m4
-autom4te*
-autom4te.*
-autom4te.cache
-bibliography.xml.bib
-bin
-cnf
-config.log
-config.status
+/aclocal.m4
+/autom4te.cache/
+/bin/
+/config.guess
+/config.status
+/config.sub
 /configure
-doc/*.css
-doc/*.js
-doc/main.aux
-doc/main.bbl
-doc/main.blg
-doc/main.brf
-doc/main.idx
-doc/main.ilg
-doc/main.ind
-doc/main.log
-doc/main.out
-doc/main.pnr
-doc/main.tex
-doc/main.toc
-doc/manual.pdf
-doc/manual.six
-gapbind14/demo/gen/
-gh-pages
-lcov*
-libtool
-libtool.m4
-ltmain.sh
-ltoptions.m4
-ltsugar.m4
-ltversion.m4
-lt~obsolete.m4
-main.xml
-new_bibliography.xml.bib
-pkgconfig.h.in~
-semigroups-config.hpp
-src/.deps
-src/.dirstamp
-src/.libs
-src/_pkgconfig.h
-src/stamp-h1
-tags
-title.xml
-tmp
-tst/workspaces/test-output.w
-wiki/
+/doc/_*.xml
+/doc/*.aux
+/doc/*.bbl
+/doc/*.blg
+/doc/*.brf
+/doc/*.css
+/doc/*.html
+/doc/*.idx
+/doc/*.ilg
+/doc/*.ind
+/doc/*.js
+/doc/*.log
+/doc/*.out
+/doc/*.pdf
+/doc/*.pnr
+/doc/*.tex
+/doc/*.toc
+/doc/*.txt
+/doc/*.xml.bib
+/doc/main.xml
+/doc/manual.lab
+/doc/manual.six
+/doc/title.xml
+/gapbind14/demo/gen/
+/gen/
+/gh-pages/
+/libsemigroups/
+/Makefile
+/src/pkgconfig.h.in
+/src/semigroups-config.hpp
diff --git a/Makefile.am b/Makefile.am
deleted file mode 100644
index b096582fe..000000000
--- a/Makefile.am
+++ /dev/null
@@ -1,120 +0,0 @@
-#
-# Semigroups
-#
-# This file is part of the build system of a GAP kernel extension.
-# Requires automake.
-#
-ACLOCAL_AMFLAGS = -I m4
-
-if WITH_INCLUDED_LIBSEMIGROUPS
-  SUBDIRS = libsemigroups
-  # the following triggers "make install" on libsemigroups
-  # note that making it a concrete file prevents this target
-  # to be needlessly re-run if libsemigroups/ is not changed.
-  BUILT_SOURCES = bin/include/libsemigroups/libsemigroups.hpp
-endif
-
-AM_CPPFLAGS = @LIBSEMIGROUPS_CFLAGS@
-
-BINARCHDIR = bin/$(GAPARCH)
-GAPINSTALLLIB = $(abs_top_srcdir)/$(BINARCHDIR)/semigroups.so
-
-lib_LTLIBRARIES = semigroups.la
-
-semigroups_la_SOURCES =  src/bipart.cpp
-semigroups_la_SOURCES += src/cong.cpp
-semigroups_la_SOURCES += src/froidure-pin-base.cpp
-semigroups_la_SOURCES += src/froidure-pin-bipart.cpp
-semigroups_la_SOURCES += src/froidure-pin-bmat.cpp
-semigroups_la_SOURCES += src/froidure-pin-fallback.cpp
-semigroups_la_SOURCES += src/froidure-pin-matrix.cpp
-semigroups_la_SOURCES += src/froidure-pin-max-plus-mat.cpp
-semigroups_la_SOURCES += src/froidure-pin-min-plus-mat.cpp
-semigroups_la_SOURCES += src/froidure-pin-pbr.cpp
-semigroups_la_SOURCES += src/froidure-pin-pperm.cpp
-semigroups_la_SOURCES += src/froidure-pin-transf.cpp
-semigroups_la_SOURCES += src/pkg.cpp
-semigroups_la_SOURCES += src/to_gap.cpp
-semigroups_la_SOURCES += gapbind14/src/gapbind14.cpp
-
-semigroups_la_CXXFLAGS = $(GAP_CFLAGS)   @LIBSEMIGROUPS_CFLAGS@ -std=gnu++14 -O3
-semigroups_la_CPPFLAGS = $(GAP_CPPFLAGS) @LIBSEMIGROUPS_CFLAGS@
-semigroups_la_CPPFLAGS += -I$(top_srcdir)/gapbind14/include
-
-if HPCOMBI_CONSTEXPR_FUN_ARGS
-semigroups_la_CPPFLAGS += -DHPCOMBI_CONSTEXPR_FUN_ARGS
-endif
-
-if LIBSEMIGROUPS_HPCOMBI_ENABLED
-semigroups_la_CXXFLAGS += $(HPCOMBI_CXXFLAGS)
-endif
-
-semigroups_la_CFLAGS = $(GAP_CFLAGS)
-
-if WITH_INCLUDED_LIBSEMIGROUPS
-# FIXME(later) all the include paths should point into bin/include/ and not to
-# the sources, or otherwise we should stop make installing into bin
-if LIBSEMIGROUPS_HPCOMBI_ENABLED
-semigroups_la_CPPFLAGS += -I$(top_srcdir)/libsemigroups/extern/HPCombi/include
-semigroups_la_CPPFLAGS += -I$(top_srcdir)/libsemigroups/extern/HPCombi/include/fallback
-endif
-semigroups_la_CPPFLAGS += -I$(top_srcdir)/libsemigroups/extern/fmt-8.0.1/include
-semigroups_la_CPPFLAGS += -I$(top_srcdir)/libsemigroups/include
-endif
-semigroups_la_CPPFLAGS += -DFMT_HEADER_ONLY
-
-if KERNEL_DEBUG
-semigroups_la_CPPFLAGS += -DDEBUG
-else
-semigroups_la_CPPFLAGS += -DNDEBUG
-endif
-
-semigroups_la_LDFLAGS = $(GAP_LDFLAGS) -module -avoid-version
-
-semigroups_la_LIBADD = @LIBSEMIGROUPS_LIBS@
-
-if SYS_IS_CYGWIN
-semigroups_la_LDFLAGS += -no-undefined -version-info 0:0:0 -Wl,$(GAPROOT)/bin/$(GAPARCH)/gap.dll
-endif
-
-# the following is only run if BUILT_SOURCES is wound up
-bin/include/libsemigroups/libsemigroups.hpp:
-	$(MAKE) -C libsemigroups install
-
-all-local: semigroups.la
-	$(mkdir_p) $(top_srcdir)/$(BINARCHDIR)
-	rm -f $(GAPINSTALLLIB)  # workaround for macOS code signing
-if SYS_IS_CYGWIN
-	cp .libs/semigroups.dll $(GAPINSTALLLIB)
-if WITH_INCLUDED_LIBSEMIGROUPS
-# Cygwin will only look in this directory for dlls
-	cp libsemigroups/.libs/cygsemigroups-*.dll $(GAPROOT)/.libs
-endif
-else
-	cp .libs/semigroups.so $(GAPINSTALLLIB)
-endif
-
-if KERNEL_DEBUG
-	@echo "SUCCESS (debug mode enabled)!"
-else
-	@echo "SUCCESS!"
-endif
-
-distclean-local:
-	rm -rf bin/*
-
-doc: doc/manual.six
-
-doc/manual.six: doc/*.xml PackageInfo.g
-	($(GAPROOT)/bin/gap.sh -A makedoc.g)
-
-lint:
-	etc/gaplint.sh
-	etc/cpplint.sh
-
-format:
-	clang-format -i src/*.hpp src/*.cpp
-
-superclean: distclean
-	git clean -xdf --exclude *.swp --exclude *.swo
-.PHONY: superclean
diff --git a/Makefile.gappkg b/Makefile.gappkg
new file mode 100644
index 000000000..30416303f
--- /dev/null
+++ b/Makefile.gappkg
@@ -0,0 +1,220 @@
+########################################################################
+#
+# The build rules in this file are intended for use by GAP packages that
+# want to build a simple GAP kernel extensions. They are based on the
+# GAP build system, and require GNU make. To use this in your GAP
+# package, `include` this file from your primary Makefile. You must also
+# set several variables beforehand:
+#
+# - GAPPATH must be set to the location of the GAP installation against
+#   which to build your package.
+# - KEXT_NAME should be the name of your kernel extension (without
+#   file extensions like .so or .dll)
+# - KEXT_SOURCES must contain a list of .c or .cc files to be linked
+#   into your kernel extension
+# - optionally, you can set KEXT_CFLAGS, KEXT_CXXFLAGS, KEXT_LDFLAGS
+# - if you are using autoconf to produce your configure script, set
+#   KEXT_USE_AUTOCONF to 1 to enable dependency rules that enable
+#   regenerating the configure script etc. when necessary
+#
+# The contents of this file are released into the public domain; hence
+# you may edit this file as you wish, bundle and distribute it with your
+# package, etc.
+#
+# If you bundle this file with your package, please try not to edit it,
+# so that we can keep it identical across all GAP packages. Instead, if
+# you find that you must edit it, please submit your changes back to
+# the GAP team, so that a future version of this file can be adjusted
+# to cover your usecase without modifications, thus ensuring you can
+# always easily update to newer version of it.
+#
+########################################################################
+
+# read GAP's build settings
+include $(GAPPATH)/sysinfo.gap
+
+# hack to support GAP <= 4.9
+ifndef GAP_KERNEL_MAJOR_VERSION
+  KEXT_CFLAGS += -I$(GAP_LIB_DIR)/src
+  KEXT_CXXFLAGS += -I$(GAP_LIB_DIR)/src
+endif
+
+# honor used supplied flags
+KEXT_CFLAGS += $(CPPFLAGS)
+KEXT_CFLAGS += $(CFLAGS)
+KEXT_CXXFLAGS += $(CPPFLAGS)
+KEXT_CXXFLAGS += $(CXXFLAGS)
+KEXT_LDFLAGS += $(LDFLAGS)
+
+# various derived settings
+KEXT_BINARCHDIR = bin/$(GAParch)
+KEXT_SO = $(KEXT_BINARCHDIR)/$(KEXT_NAME).so
+
+# the following settings are provided by sysinfo.gap in GAP >= 4.12;
+# for compatibility with older GAP version (at least 4.9, 4.10, 4.11)
+# we try to "guess" suitable values here
+GAP ?= $(GAPPATH)/gap
+GAC ?= $(GAPPATH)/gac
+GAP_OBJEXT ?= lo
+
+# override KEXT_RECONF if your package needs a different invocation
+# for reconfiguring (e.g. `./config.status --recheck` for autoconf)
+ifdef KEXT_USE_AUTOCONF
+KEXT_RECONF ?= ./config.status Makefile
+else
+KEXT_RECONF ?= ./configure "$(GAPPATH)"
+endif
+
+# default target
+all: $(KEXT_SO)
+.PHONY: all
+
+########################################################################
+# Object files
+# For each file FOO.c in SOURCES, add gen/FOO.$(GAP_OBJEXT) to KEXT_OBJS
+# and similar for .cc files
+########################################################################
+KEXT_OBJS = $(patsubst %.s,gen/%.$(GAP_OBJEXT), \
+            $(patsubst %.cpp,gen/%.$(GAP_OBJEXT), \
+            $(patsubst %.c,gen/%.$(GAP_OBJEXT), \
+                $(KEXT_SOURCES))))
+
+########################################################################
+# Quiet rules.
+#
+# Replace regular output with quiet messages, unless V is set,
+# e.g. "make V=1"
+########################################################################
+ifneq ($(findstring $(MAKEFLAGS),s),s)
+ifndef V
+QUIET_GAC     = @echo "   GAC     $< => $@";>/dev/null # keep the trailing space!
+endif
+endif
+
+########################################################################
+# Rules for automatic header dependency tracking.
+# This is based on the GAP build system.
+########################################################################
+
+# List of all (potential) dependency files, derived from KEXT_OBJS
+KEXT_DEPFILES = $(patsubst %.$(GAP_OBJEXT),%.d,$(KEXT_OBJS))
+
+# Include the dependency tracking files
+-include $(KEXT_DEPFILES)
+
+# Mark *.d files as PHONY. This stops make from trying to recreate them
+# (which it can't), and in particular from looking for potential source
+# files. This can save quite a bit of disk access time.
+.PHONY: $(KEXT_DEPFILES)
+
+# The following flags instruct the compiler to enable advanced
+# dependency tracking. Supported by GCC 3 and newer; clang; Intel C
+# compiler; and more.
+KEXT_DEPFLAGS = -MQ "$@" -MMD -MP -MF $(@D)/$(*F).d
+
+# build rule for C code
+# The dependency on Makefile ensures that re-running configure recompiles everything
+gen/%.$(GAP_OBJEXT): %.c Makefile
+	@mkdir -p $(@D)
+	$(QUIET_GAC)$(GAC) -d -p "$(KEXT_DEPFLAGS)" -p "$(KEXT_CFLAGS)" -c $< -o $@
+
+# build rule for C++ code
+# The dependency on Makefile ensures that re-running configure recompiles everything
+gen/%.$(GAP_OBJEXT): %.cpp Makefile
+	@mkdir -p $(@D)
+	$(QUIET_GAC)$(GAC) -d -p "$(KEXT_DEPFLAGS)" -p "$(KEXT_CXXFLAGS)" -c $< -o $@
+
+# build rule for assembler code
+# The dependency on Makefile ensures that re-running configure recompiles everything
+gen/%.$(GAP_OBJEXT): %.s Makefile
+	@mkdir -p $(@D)
+	$(QUIET_GAC)$(GAC) -d -p "$(KEXT_DEPFLAGS)" -p "$(KEXT_CFLAGS)" -c $< -o $@
+
+# build rule for linking all object files together into a kernel extension
+$(KEXT_SO): $(KEXT_OBJS)
+	@mkdir -p $(@D)
+	$(QUIET_GAC)$(GAC) -d -p "$(KEXT_DEPFLAGS)" -P "$(KEXT_LDFLAGS)" $(KEXT_OBJS) -o $@
+
+# hook into `make clean`
+clean: clean-kext
+clean-kext:
+	rm -rf $(KEXT_BINARCHDIR) gen
+
+# hook into `make distclean`
+distclean: distclean-kext
+distclean-kext:
+	rm -rf bin gen Makefile
+	rm -rf doc/_*.xml
+	rm -rf doc/*.aux doc/*.bbl doc/*.blg doc/*.brf doc/*.idx doc/*.idx
+	rm -rf doc/*.ilg doc/*.ind doc/*.log doc/*.out doc/*.pnr doc/*.toc
+
+# hook into `make doc`
+doc: doc-kext
+doc-kext:
+	$(GAP) --quitonbreak -b -q < makedoc.g
+
+# hook into `make check`
+check: check-kext
+check-kext:
+	$(GAP) tst/testall.g
+
+# re-run configure if configure, Makefile.in or GAP itself changed
+Makefile: configure Makefile.in $(GAPPATH)/sysinfo.gap
+	$(KEXT_RECONF)
+
+ifdef KEXT_USE_AUTOCONF
+
+# react to modifications of the build system
+configure_deps = configure.ac $(wildcard m4/*.m4)
+
+ifneq ($(MAINTAINER_MODE),no)
+configure: $(configure_deps)
+	@if command -v autoconf >/dev/null 2>&1 ; then \
+	   echo "running autoconf" ; \
+	   autoconf ; \
+	 else \
+	   echo "autoconf not available, proceeding with stale configure" ; \
+	 fi
+endif # MAINTAINER_MODE
+
+# re-run configure if configure, Makefile.in or GAP itself changed
+config.status: configure $(GAPPATH)/sysinfo.gap
+	./config.status --recheck
+
+# update Makefile if config.status changed
+Makefile: config.status
+
+gen/pkgconfig.h: gen/pkgconfig.h.stamp
+	@if test ! -f $@; then rm -f $<; else :; fi
+	@if test ! -f $@; then $(MAKE) $<; else :; fi
+
+gen/pkgconfig.h.stamp: src/pkgconfig.h.in config.status
+	@rm -f $@
+	@mkdir -p $(@D)
+	./config.status gen/pkgconfig.h
+	echo > $@
+
+ifneq ($(MAINTAINER_MODE),no)
+src/pkgconfig.h.in: $(configure_deps)
+	@if command -v autoheader >/dev/null 2>&1 ; then \
+	   mkdir -p $(@D) ; \
+	   echo "running autoheader" ; \
+	   autoheader ; \
+	   rm -f gen/pkgconfig.h.stamp ; \
+	 else \
+	   echo "autoheader not available, proceeding with stale config.h" ; \
+	 fi
+	touch $@
+endif # MAINTAINER_MODE
+
+endif # KEXT_USE_AUTOCONF
+
+.PHONY: check clean distclean doc
+.PHONY: check-kext clean-kext distclean-kext doc-kext
+
+########################################################################
+# Makefile debugging trick:
+# call print-VARIABLE to see the runtime value of any variable
+########################################################################
+print-%:
+	@echo '$*=$($*)'
diff --git a/Makefile.in b/Makefile.in
new file mode 100644
index 000000000..f7b64c0f2
--- /dev/null
+++ b/Makefile.in
@@ -0,0 +1,110 @@
+#
+# Makefile rules for the semigroups package
+#
+KEXT_NAME = semigroups
+
+KEXT_CXXFLAGS = @LIBSEMIGROUPS_CFLAGS@ -std=gnu++14 -O3
+KEXT_LDFLAGS = -lstdc++  # add C++ library
+
+# configure settings
+GAPPATH = @GAPROOT@
+HPCOMBI_CONSTEXPR_FUN_ARGS = @HPCOMBI_CONSTEXPR_FUN_ARGS@
+LIBSEMIGROUPS_HPCOMBI_ENABLED = @LIBSEMIGROUPS_HPCOMBI_ENABLED@
+WITH_INCLUDED_LIBSEMIGROUPS = @WITH_INCLUDED_LIBSEMIGROUPS@
+SYS_IS_CYGWIN = @SYS_IS_CYGWIN@
+
+# sources
+KEXT_SOURCES =  src/bipart.cpp
+KEXT_SOURCES += src/cong.cpp
+KEXT_SOURCES += src/froidure-pin-base.cpp
+KEXT_SOURCES += src/froidure-pin-bipart.cpp
+KEXT_SOURCES += src/froidure-pin-bmat.cpp
+KEXT_SOURCES += src/froidure-pin-fallback.cpp
+KEXT_SOURCES += src/froidure-pin-matrix.cpp
+KEXT_SOURCES += src/froidure-pin-max-plus-mat.cpp
+KEXT_SOURCES += src/froidure-pin-min-plus-mat.cpp
+KEXT_SOURCES += src/froidure-pin-pbr.cpp
+KEXT_SOURCES += src/froidure-pin-pperm.cpp
+KEXT_SOURCES += src/froidure-pin-transf.cpp
+KEXT_SOURCES += src/pkg.cpp
+KEXT_SOURCES += src/to_gap.cpp
+KEXT_SOURCES += gapbind14/src/gapbind14.cpp
+
+KEXT_CPPFLAGS = -Igapbind14/include/
+
+ifdef HPCOMBI_CONSTEXPR_FUN_ARGS
+KEXT_CPPFLAGS += -DHPCOMBI_CONSTEXPR_FUN_ARGS
+endif
+
+ifdef LIBSEMIGROUPS_HPCOMBI_ENABLED
+KEXT_CXXFLAGS += $(HPCOMBI_CXXFLAGS)
+endif
+
+ifdef WITH_INCLUDED_LIBSEMIGROUPS
+KEXT_LDFLAGS += -Wl,-rpath,bin/lib
+# FIXME(later) all the include paths should point into bin/include/ and not to
+# the sources, or otherwise we should stop make installing into bin
+ifdef LIBSEMIGROUPS_HPCOMBI_ENABLED
+KEXT_CPPFLAGS += -Ilibsemigroups/extern/HPCombi/include
+KEXT_CPPFLAGS += -Ilibsemigroups/extern/HPCombi/include/fallback
+endif
+KEXT_CPPFLAGS += -Ilibsemigroups/extern/fmt-8.0.1/include
+KEXT_CPPFLAGS += -Ilibsemigroups/include
+endif
+KEXT_CPPFLAGS += -DFMT_HEADER_ONLY
+
+ifdef KERNEL_DEBUG
+KEXT_CPPFLAGS += -DDEBUG
+else
+KEXT_CPPFLAGS += -DNDEBUG
+endif
+
+KEXT_CXXFLAGS += $(KEXT_CPPFLAGS) # HACK: there is no KEXT_CPPFLAGS
+
+KEXT_LDFLAGS += @LIBSEMIGROUPS_LIBS@
+
+# HACK: On cygwin, add this flag to work around issues where fork() sometimes
+# fails on Cygwin when semigroups.so is loaded into GAP. This will hopefully
+# become unnecessary with GAP 4.13, which will automatically add this to the
+# flags.
+ifdef SYS_IS_CYGWIN
+KEXT_LDFLAGS += -Wl,--enable-auto-image-base
+endif
+
+# include shared GAP package build system
+KEXT_USE_AUTOCONF = 1
+include Makefile.gappkg
+
+# ensure pkgconfig.h is built
+$(KEXT_OBJS): gen/pkgconfig.h
+
+ifdef WITH_INCLUDED_LIBSEMIGROUPS
+# ensure libsemigroups is installed into bin before compiling
+$(KEXT_OBJS): bin/include/libsemigroups/libsemigroups.hpp
+
+# the following is only run if BUILT_SOURCES is wound up
+bin/include/libsemigroups/libsemigroups.hpp:
+	$(MAKE) -C libsemigroups install
+	# Cygwin only looks for DLLs in the same directory as the executable
+	# resides in. The following achieves that assuming that the GAP
+	# being used was self-compiled by the user. If the GAP build system
+	# changes to stop using GNU libtool, this will have to be adjusted.
+	if test -f bin/bin/cygsemigroups*.dll ; then cp bin/bin/cygsemigroups*.dll $(GAPPATH)/.libs ; fi
+
+endif
+
+clean:
+	find . -name '*.gcda' -delete
+
+lint:
+	etc/gaplint.sh
+	etc/cpplint.sh
+
+format:
+	clang-format -i src/*.[hc]
+
+.PHONY: lint format
+
+superclean: distclean
+	git clean -xdf --exclude *.swp --exclude *.swo
+.PHONY: superclean
diff --git a/configure.ac b/configure.ac
index 11c396ef2..a7c84aac0 100644
--- a/configure.ac
+++ b/configure.ac
@@ -9,26 +9,12 @@ dnl ##
 dnl ## Setup autoconf
 dnl ##
 AC_PREREQ([2.68])
-AC_INIT([semigroups], m4_esyscmd([tr -d '\n' < .VERSION]))
+AC_INIT([semigroups], [GAP package])
 AC_CONFIG_SRCDIR([src/pkg.cpp])
-AC_CONFIG_HEADERS([src/_pkgconfig.h:cnf/pkgconfig.h.in])
+AC_CONFIG_HEADERS([gen/pkgconfig.h:src/pkgconfig.h.in])
 AC_CONFIG_MACRO_DIR([m4])
-AC_CONFIG_AUX_DIR([cnf])
 
-dnl ##
-dnl ## Get canonical host info
-dnl ##
-AC_CANONICAL_HOST
-AC_CANONICAL_TARGET
-
-dnl ##
-dnl ## Setup automake
-dnl ##
-AM_INIT_AUTOMAKE([1.11 -Wall foreign subdir-objects nostdinc])
-AM_SILENT_RULES([yes])
-AM_PROG_AR
-
-AX_PREFIX_CONFIG_H([src/semigroups-config.hpp],[],[src/_pkgconfig.h])
+AX_PREFIX_CONFIG_H([src/semigroups-config.hpp],[semigroups],[gen/pkgconfig.h])
 
 dnl ## abs_top_builddir seems to hold the top build dir for the subpackage
 dnl ## libsemigroups which is why this contains ../ 
@@ -42,12 +28,6 @@ AC_LANG([C++])
 
 AX_CXX_COMPILE_STDCXX_14(,[mandatory])
 
-dnl ##
-dnl ## Setup libtool (for building the GAP kernel extension)
-dnl ##
-LT_PREREQ([2.4.2])
-LT_INIT([disable-static dlopen win32-dll])
-
 dnl ##
 dnl ## Locate the GAP root dir
 dnl ##
@@ -63,10 +43,9 @@ dnl ##
 dnl ## Detect Windows resp. Cygwin
 dnl ##
 case $host_os in
-  *cygwin* ) CYGWIN=yes;;
-         * ) CYGWIN=no;;
+  *cygwin* ) AC_SUBST(SYS_IS_CYGWIN, yes);;
 esac
-AM_CONDITIONAL([SYS_IS_CYGWIN], [test "$CYGWIN" = "yes"])
+
 
 dnl ## Check for libsemigroups
 AX_CHECK_LIBSEMIGROUPS
@@ -79,11 +58,11 @@ AC_ARG_ENABLE([debug],
     )
 AC_MSG_CHECKING([whether to enable debug mode])
 AC_MSG_RESULT([$enable_debug])
-
-AM_CONDITIONAL([KERNEL_DEBUG], [test "x$enable_debug" = xyes])
+ERNEL_DEBUG=$enable_debug
+AC_SUBST(KERNEL_DEBUG)
 
 # Check if HPCombi is enable, and available
-AX_CHECK_HPCOMBI()
+AX_CHECK_HPCOMBI
 
 dnl ##
 dnl ## Output everything
diff --git a/gapbind14/.gitignore b/gapbind14/.gitignore
deleted file mode 100644
index b0da25eab..000000000
--- a/gapbind14/.gitignore
+++ /dev/null
@@ -1,60 +0,0 @@
-/doc/chap*.html
-/doc/chap*.txt
-/doc/*.css
-/doc/*.js
-/doc/chooser.html
-/doc/*.aux
-/doc/*.bbl
-/doc/*.blg
-/doc/*.brf
-/doc/*.idx
-/doc/*.ilg
-/doc/*.ind
-/doc/*.lab
-/doc/*.log
-/doc/*.out
-/doc/*.pnr
-/doc/*.six
-/doc/*.tex
-/doc/*.toc
-/doc/manual.pdf
-
-.deps/
-.dirstamp
-.libs/
-
-/aclocal.m4
-/autom4te.cache/
-/bin/
-/config.log
-/config.status
-/configure
-/lib/
-/libtool
-/cnf/dd
-/cnf/ar-lib
-/cnf/compile
-/cnf/config.guess
-/cnf/config.sub
-/cnf/depcomp
-/cnf/install-sh
-/cnf/ltmain.sh
-/cnf/missing
-/cnf/pkgconfig.h.in
-/cnf/m4/libtool.m4
-/cnf/m4/ltoptions.m4
-/cnf/m4/ltsugar.m4
-/cnf/m4/ltversion.m4
-/cnf/m4/lt~obsolete.m4
-/Makefile
-/Makefile.in
-/src/pkgconfig.h
-/src/stamp-h1
-
-*.la
-src/*.lo
-
-/tmp/
-/gh-pages/
-*.so
-demo/gen
diff --git a/gapbind14/CPPLINT.cfg b/gapbind14/CPPLINT.cfg
index b62bcbb4b..1f8f5cc6f 100644
--- a/gapbind14/CPPLINT.cfg
+++ b/gapbind14/CPPLINT.cfg
@@ -2,4 +2,4 @@ set noparent
 filter=-build/c++11,-build/include_subdir,-runtime/indentation_namespace,-runtime/references
 linelength=80
 root=pkg
-exclude_files=(semigroups-config.hpp|_pkgconfig.h)
+exclude_files=(semigroups-config.hpp|pkgconfig.h)
diff --git a/gapbind14/demo/.gitignore b/gapbind14/demo/.gitignore
index eca8fdb10..bda691f01 100644
--- a/gapbind14/demo/.gitignore
+++ b/gapbind14/demo/.gitignore
@@ -1 +1,4 @@
-src/gapbind14.cc
\ No newline at end of file
+/Makefile
+/bin/
+/src/gapbind14.cc
+/doc/
diff --git a/m4/ax_check_hpcombi.m4 b/m4/ax_check_hpcombi.m4
index 156b2eb83..1594192e8 100644
--- a/m4/ax_check_hpcombi.m4
+++ b/m4/ax_check_hpcombi.m4
@@ -28,7 +28,7 @@ AC_DEFUN([AX_CHECK_HPCOMBI], [
   AC_MSG_RESULT([$enable_hpcombi])
 
   AS_IF([test "x$enable_hpcombi" = xyes],
-        [AC_CHECK_FILE([$srcdir/extern/HPCombi/VERSION], 
+        [AS_IF([test -f $srcdir/extern/HPCombi/VERSION], 
                        [], 
                        [AC_MSG_WARN([HPCombi is not available])
                        [enable_hpcombi=no]])])
@@ -96,7 +96,8 @@ AC_DEFUN([AX_CHECK_HPCOMBI], [
         [AC_DEFINE([HPCOMBI_ENABLED], [1], [define if building with HPCombi])])
 
   dnl # the following is used in Makefile.am
-  AM_CONDITIONAL([LIBSEMIGROUPS_HPCOMBI_ENABLED], [test "x$enable_hpcombi" = xyes])
+  AS_IF([test "x$enable_hpcombi" = xyes],
+        AC_SUBST(LIBSEMIGROUPS_HPCOMBI_ENABLED, yes))
 
   dnl # check for HPCombi's preprocessor macro
   AS_IF([test "x$enable_hpcombi" = xyes], 
@@ -112,9 +113,9 @@ AC_DEFUN([AX_CHECK_HPCOMBI], [
                    )
    AC_MSG_RESULT([$hpcombi_constexpr_fun_args])])
 
-  AM_CONDITIONAL([HPCOMBI_CONSTEXPR_FUN_ARGS], 
-                 [test "x$hpcombi_constexpr_fun_args" = xyes])
-    
+  AS_IF([test "x$hpcombi_constexpr_fun_args" = xyes],
+        AC_SUBST(HPCOMBI_CONSTEXPR_FUN_ARGS, yes))
+
   AS_IF([test "x$enable_hpcombi" = xyes],
         AC_SUBST(ax_hpcombi_cxxflags_variable))
 ])
diff --git a/m4/ax_check_libsemigroup.m4 b/m4/ax_check_libsemigroup.m4
index 0133737d2..de5173451 100644
--- a/m4/ax_check_libsemigroup.m4
+++ b/m4/ax_check_libsemigroup.m4
@@ -19,25 +19,25 @@ AC_DEFUN([AX_CHECK_LIBSEMIGROUPS], [
   fi
   if test "$need_included_libsemigroups" = yes;  then
 	AC_MSG_NOTICE([using included libsemigroups...])
-  	AC_CHECK_FILE(
-   		[libsemigroups/include/libsemigroups/libsemigroups.hpp],
+  	AS_IF(
+   		[test -f libsemigroups/include/libsemigroups/libsemigroups.hpp],
    		[],
    		dnl Temporary workaround for backward compatibility with
    		dnl libsemigroups pre PR 172: Includes in libsemigroups/
-   		[AC_CHECK_FILE(
-   		   [libsemigroups/include/libsemigroups.hpp],
+   		[AS_IF(
+   		   [test -f libsemigroups/include/libsemigroups.hpp],
                    [],
                    [AC_MSG_ERROR([libsemigroups is required, clone or download the repo from https://github.com/libsemigroups/libsemigroups into this directory])])])
 
         dnl Temporary workaround for compatibility with dev version of
         dnl libsemigroups which doesn't contain .VERSION file by default
-	AC_CHECK_FILE(
-   		[libsemigroups/.VERSION],
+	AS_IF(
+   		[test -f libsemigroups/.VERSION],
    		[],
-                [AC_CHECK_FILE([libsemigroups/etc/version-number.sh], 
-                               [cd libsemigroups && etc/version-number.sh > .TMP_VERSION && mv .TMP_VERSION .VERSION && cd ..],
-                               [AC_MSG_ERROR([cannot determine the version of libsemigroups])])])
-
+        [AS_IF([test -f libsemigroups/etc/version-number.sh], 
+           [cd libsemigroups && etc/version-number.sh > .TMP_VERSION && mv .TMP_VERSION .VERSION && cd ..],
+           [AC_MSG_ERROR([cannot determine the version of libsemigroups])])])
+    
 	AC_MSG_CHECKING([libsemigroups version])
 	FOUND_LIBSEMIGROUPS_VERSION="$(cat libsemigroups/.VERSION)"
 	AC_MSG_RESULT([$FOUND_LIBSEMIGROUPS_VERSION])
@@ -47,13 +47,14 @@ AC_DEFUN([AX_CHECK_LIBSEMIGROUPS], [
                    [],
                    [AC_MSG_ERROR([libsemigroups version $REQUI_LIBSEMIGROUPS_VERSION or higher is required])]
                   )
-	AC_SUBST(LIBSEMIGROUPS_CFLAGS, ['-I./bin/include -I./bin/include/libsemigroups'])
-	AC_SUBST(LIBSEMIGROUPS_LIBS, ['bin/lib/libsemigroups.la'])
+        AC_SUBST(LIBSEMIGROUPS_CFLAGS, ['-I./bin/include -I./bin/include/libsemigroups'])
+        AC_SUBST(LIBSEMIGROUPS_LIBS, ['-L./bin/lib -lsemigroups'])
         AC_CONFIG_SUBDIRS([libsemigroups])
   else 
         LIBSEMIGROUPS_VERSION="$(pkg-config --modversion libsemigroups)"
 	AC_MSG_NOTICE([using external libsemigroups $LIBSEMIGROUPS_VERSION])
   fi
 
-  AM_CONDITIONAL([WITH_INCLUDED_LIBSEMIGROUPS], [test "$need_included_libsemigroups" = yes])
+  AS_IF([test "x$need_included_libsemigroups" = xyes],
+        AC_SUBST(WITH_INCLUDED_LIBSEMIGROUPS, yes))
 ])
diff --git a/src/CPPLINT.cfg b/src/CPPLINT.cfg
index 4ced5cad6..4d14976a7 100644
--- a/src/CPPLINT.cfg
+++ b/src/CPPLINT.cfg
@@ -2,4 +2,4 @@ set noparent
 filter=-build/c++11,-build/c++14,-build/include_subdir,-runtime/indentation_namespace,-runtime/references,-readability/todo
 linelength=80
 root=../..
-exclude_files=(semigroups-config.hpp|_pkgconfig.h)
+exclude_files=(semigroups-config.hpp|pkgconfig.h)