diff --git a/.gitignore b/.gitignore
index 0d06ec435..654b88ca8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,11 +1,12 @@
-*.DS_Store
-*.Plo
-*.Tpo
+.ipynb_checkpoints
+*.a
 *.aux
 *.bbl
 *.blg
 *.brf
 *.digraphs
+*.DS_Store
+*.dylib
 *.g6
 *.gcda
 *.gcno
@@ -22,58 +23,38 @@
 *.o
 *.out
 *.pdf
+*.Plo
 *.pnr
 *.pyc
 *.six
 *.status
 *.sub
+*.swo
 *.swp
 *.synctex.gz
 *.tex
 *.toc
 *.top
+*.Tpo
 *.tui
 *.txt
-.dirstamp
-.libs/*
-Makefile
-Makefile.in
+/doc/*.css
+/doc/*.js
 aclocal.m4
 autom4te.*
-bin/*
-cnf/*
+bin/
+bliss
+compile
 configure
+coverage
+depcomp
 digraphs-config.h
 digraphs-lib
+gen/
 gh-pages/
-libtool
-ltmain.sh
-m4/*
-planarity
-src/.deps/*
-src/.libs/*
-src/_pkgconfig.h
-extern/edge-addition-planarity-suite-Version_*/.libs
-extern/edge-addition-planarity-suite-Version_*/c/.deps
-extern/edge-addition-planarity-suite-Version_*/m4
-src/stamp-h1
-tags
-tst/out/*
-data/digraphs-lib-0.5
-gh-pages/
+Makefile
 manual.lab
-ltmain.sh
-.libs/**/Info.plist
-digraphs-config.h
-compile
-depcomp
-install-sh
 missing
-*.swo
-coverage
-.ipynb_checkpoints
-bliss
-*.a
-*.dylib
-/doc/*.js
-/doc/*.css
+src/pkgconfig.h.in
+tags
+tst/out/
diff --git a/Makefile.am b/Makefile.am
deleted file mode 100644
index 333426a2f..000000000
--- a/Makefile.am
+++ /dev/null
@@ -1,139 +0,0 @@
-#
-# digraphs:
-#
-# This file is part of the build system of a GAP kernel extension.
-# Requires automake.
-#
-
-ACLOCAL_AMFLAGS = -I m4
-
-if WITH_INCLUDED_PLANARITY 
-  SUBDIRS = @PLANARITY_SUITE_DIR@
-  PLANAR_INCLUDE = -I$(top_srcdir)/@PLANARITY_SUITE_DIR@/
-endif
-
-if WITH_INCLUDED_BLISS
-  DIGRAPHS_INCLUDE = -I$(top_srcdir)/extern/
-endif
-
-BINARCHDIR = bin/$(GAPARCH)
-GAPINSTALLLIB = $(abs_top_srcdir)/$(BINARCHDIR)
-
-lib_LTLIBRARIES = digraphs.la
-
-pkginclude_HEADERS =  src/bitarray.h
-pkginclude_HEADERS += src/conditions.h
-pkginclude_HEADERS += src/digraphs-debug.h
-pkginclude_HEADERS += src/digraphs.h
-pkginclude_HEADERS += src/homos-graphs.h
-pkginclude_HEADERS += src/homos.h
-pkginclude_HEADERS += src/cliques.h
-pkginclude_HEADERS += src/perms.h
-pkginclude_HEADERS += src/planar.h
-pkginclude_HEADERS += src/schreier-sims.h
-
-if WITH_INCLUDED_BLISS
-  pkginclude_HEADERS += extern/bliss-0.73/bignum.hh
-  pkginclude_HEADERS += extern/bliss-0.73/bliss_C.h
-  pkginclude_HEADERS += extern/bliss-0.73/defs.hh
-  pkginclude_HEADERS += extern/bliss-0.73/graph.hh
-  pkginclude_HEADERS += extern/bliss-0.73/heap.hh
-  pkginclude_HEADERS += extern/bliss-0.73/kqueue.hh
-  pkginclude_HEADERS += extern/bliss-0.73/kstack.hh
-  pkginclude_HEADERS += extern/bliss-0.73/orbit.hh
-  pkginclude_HEADERS += extern/bliss-0.73/partition.hh
-  pkginclude_HEADERS += extern/bliss-0.73/timer.hh
-  pkginclude_HEADERS += extern/bliss-0.73/uintseqhash.hh
-  pkginclude_HEADERS += extern/bliss-0.73/utils.hh
-endif
-
-digraphs_la_SOURCES =  src/digraphs.c
-digraphs_la_SOURCES += src/bitarray.c
-digraphs_la_SOURCES += src/conditions.c
-digraphs_la_SOURCES += src/homos.c
-digraphs_la_SOURCES += src/cliques.c
-digraphs_la_SOURCES += src/homos-graphs.c
-digraphs_la_SOURCES += src/perms.c
-digraphs_la_SOURCES += src/planar.c
-digraphs_la_SOURCES += src/schreier-sims.c
-
-if WITH_INCLUDED_BLISS
-  digraphs_la_SOURCES += extern/bliss-0.73/defs.cc
-  digraphs_la_SOURCES += extern/bliss-0.73/graph.cc
-  digraphs_la_SOURCES += extern/bliss-0.73/partition.cc
-  digraphs_la_SOURCES += extern/bliss-0.73/orbit.cc
-  digraphs_la_SOURCES += extern/bliss-0.73/uintseqhash.cc
-  digraphs_la_SOURCES += extern/bliss-0.73/heap.cc
-  digraphs_la_SOURCES += extern/bliss-0.73/timer.cc
-  digraphs_la_SOURCES += extern/bliss-0.73/utils.cc
-  digraphs_la_SOURCES += extern/bliss-0.73/bliss_C.cc
-endif
-
-digraphs_la_CPPFLAGS =  $(GAP_CPPFLAGS)
-digraphs_la_CPPFLAGS += $(CODE_COVERAGE_CPPFLAGS)
-
-digraphs_la_CXXFLAGS =  $(PLANAR_INCLUDE) $(DIGRAPHS_INCLUDE) 
-digraphs_la_CXXFLAGS += $(CODE_COVERAGE_CXXFLAGS)
-digraphs_la_CXXFLAGS += $(WARNING_CXXFLAGS)
-
-digraphs_la_CFLAGS =  $(GAP_CFLAGS) $(PLANAR_INCLUDE) $(DIGRAPHS_INCLUDE)
-digraphs_la_CFLAGS += $(CODE_COVERAGE_CFLAGS)
-digraphs_la_CFLAGS += $(WARNING_CFLAGS)
-
-digraphs_la_LDFLAGS  =  $(GAP_LDFLAGS) -module -avoid-version
-
-if WITH_INCLUDED_PLANARITY
-digraphs_la_LIBADD = @PLANARITY_SUITE_DIR@/libplanarity.la
-endif
-
-if SYS_IS_CYGWIN
-digraphs_la_LDFLAGS += -no-undefined -version-info 0:0:0 -Wl,$(GAPROOT)/bin/$(GAPARCH)/gap.dll
-endif
-
-all-local: digraphs.la
-	$(mkdir_p) $(top_srcdir)/$(BINARCHDIR) $(top_srcdir)/bin/lib
-if WITH_INCLUDED_PLANARITY
-	rm -f $(top_srcdir)/bin/lib/*  # workaround for macOS code signing
-	cp -RL @PLANARITY_SUITE_DIR@/.libs/*  $(top_srcdir)/bin/lib/
-endif
-	rm -f $(GAPINSTALLLIB)/digraphs.so  # workaround for macOS code signing
-if SYS_IS_CYGWIN
-	cp .libs/digraphs.dll $(GAPINSTALLLIB)/digraphs.so
-if WITH_INCLUDED_PLANARITY
-	cp bin/lib/cygplanarity-0.dll $(GAPROOT)/.libs
-endif
-else
-	cp .libs/digraphs.so $(GAPINSTALLLIB)/
-endif
-if KERNEL_DEBUG
-	@echo "SUCCESS (debug mode enabled)!"
-else
-	@echo "SUCCESS!"
-endif
-
-clean-local:
-	find . -name '*.gcda' -delete
-
-distclean-local:
-	rm -f *.tmp
-	rm -f coverage.info
-	rm -rf coverage/*
-	rm -rf bin/*
-
-doc: doc/manual.six
-
-doc/manual.six: doc/*.xml PackageInfo.g
-	($(GAPROOT)/bin/gap.sh -A makedoc.g)
-
-lint:
-	etc/gaplint.sh
-	etc/cpplint.sh
-
-format:
-	clang-format -i src/*.[hc]
-
-.PHONY: debug, lint, format
-
-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..6e3491e28
--- /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), \
+            $(patsubst %.cc,gen/%.$(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): %.cc 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..c88e97118
--- /dev/null
+++ b/Makefile.in
@@ -0,0 +1,103 @@
+#
+# Makefile rules for the digraphs package
+#
+KEXT_NAME = digraphs
+
+KEXT_CFLAGS = @CODE_COVERAGE_CFLAGS@ @WARNING_CFLAGS@
+KEXT_CXXFLAGS = @CODE_COVERAGE_CXXFLAGS@ @WARNING_CXXFLAGS@
+KEXT_LDFLAGS = @CODE_COVERAGE_LDFLAGS@
+
+KEXT_LDFLAGS += -lstdc++  # for bliss: add C++ library
+
+# configure settings
+GAPPATH = @GAPROOT@
+WITH_INCLUDED_BLISS = @WITH_INCLUDED_BLISS@
+WITH_INCLUDED_PLANARITY = @WITH_INCLUDED_PLANARITY@
+PLANARITY_SUITE_DIR = @PLANARITY_SUITE_DIR@
+
+# sources
+KEXT_SOURCES =  src/digraphs.c
+KEXT_SOURCES += src/bitarray.c
+KEXT_SOURCES += src/conditions.c
+KEXT_SOURCES += src/homos.c
+KEXT_SOURCES += src/cliques.c
+KEXT_SOURCES += src/homos-graphs.c
+KEXT_SOURCES += src/perms.c
+KEXT_SOURCES += src/planar.c
+KEXT_SOURCES += src/schreier-sims.c
+
+ifdef WITH_INCLUDED_BLISS
+  KEXT_SOURCES += extern/bliss-0.73/defs.cc
+  KEXT_SOURCES += extern/bliss-0.73/graph.cc
+  KEXT_SOURCES += extern/bliss-0.73/partition.cc
+  KEXT_SOURCES += extern/bliss-0.73/orbit.cc
+  KEXT_SOURCES += extern/bliss-0.73/uintseqhash.cc
+  KEXT_SOURCES += extern/bliss-0.73/heap.cc
+  KEXT_SOURCES += extern/bliss-0.73/timer.cc
+  KEXT_SOURCES += extern/bliss-0.73/utils.cc
+  KEXT_SOURCES += extern/bliss-0.73/bliss_C.cc
+
+  KEXT_CFLAGS += -Iextern
+else
+  KEXT_LDFLAGS += -lbliss
+endif
+
+
+ifdef WITH_INCLUDED_PLANARITY
+  KEXT_SOURCES += $(PLANARITY_SUITE_DIR)/c/graphDFSUtils.c
+  KEXT_SOURCES += $(PLANARITY_SUITE_DIR)/c/graphDrawPlanar.c
+  KEXT_SOURCES += $(PLANARITY_SUITE_DIR)/c/graphDrawPlanar_Extensions.c
+  KEXT_SOURCES += $(PLANARITY_SUITE_DIR)/c/graphEmbed.c
+  KEXT_SOURCES += $(PLANARITY_SUITE_DIR)/c/graphExtensions.c
+  KEXT_SOURCES += $(PLANARITY_SUITE_DIR)/c/graphIO.c
+  KEXT_SOURCES += $(PLANARITY_SUITE_DIR)/c/graphIsolator.c
+  KEXT_SOURCES += $(PLANARITY_SUITE_DIR)/c/graphK23Search.c
+  KEXT_SOURCES += $(PLANARITY_SUITE_DIR)/c/graphK23Search_Extensions.c
+  KEXT_SOURCES += $(PLANARITY_SUITE_DIR)/c/graphK33Search.c
+  KEXT_SOURCES += $(PLANARITY_SUITE_DIR)/c/graphK33Search_Extensions.c
+  KEXT_SOURCES += $(PLANARITY_SUITE_DIR)/c/graphK4Search.c
+  KEXT_SOURCES += $(PLANARITY_SUITE_DIR)/c/graphK4Search_Extensions.c
+  KEXT_SOURCES += $(PLANARITY_SUITE_DIR)/c/graphNonplanar.c
+  KEXT_SOURCES += $(PLANARITY_SUITE_DIR)/c/graphOuterplanarObstruction.c
+  KEXT_SOURCES += $(PLANARITY_SUITE_DIR)/c/graphTests.c
+  KEXT_SOURCES += $(PLANARITY_SUITE_DIR)/c/graphUtils.c
+  KEXT_SOURCES += $(PLANARITY_SUITE_DIR)/c/listcoll.c
+  KEXT_SOURCES += $(PLANARITY_SUITE_DIR)/c/planarityRandomGraphs.c
+  KEXT_SOURCES += $(PLANARITY_SUITE_DIR)/c/planaritySpecificGraph.c
+  KEXT_SOURCES += $(PLANARITY_SUITE_DIR)/c/planarityUtils.c
+  KEXT_SOURCES += $(PLANARITY_SUITE_DIR)/c/stack.c
+
+  KEXT_CFLAGS += -I$(PLANARITY_SUITE_DIR)
+else
+  KEXT_LDFLAGS += -lplanarity
+endif
+
+
+# include shared GAP package build system
+KEXT_USE_AUTOCONF = 1
+include Makefile.gappkg
+
+# ensure pkgconfig.h is built
+$(KEXT_OBJS): gen/pkgconfig.h
+
+clean:
+	find . -name '*.gcda' -delete
+
+distclean:
+	rm -f *.tmp
+	rm -f coverage.info
+	rm -rf coverage/*
+	rm -rf bin/*
+
+lint:
+	etc/gaplint.sh
+	etc/cpplint.sh
+
+format:
+	clang-format -i src/*.[hc]
+
+.PHONY: debug lint format
+
+superclean: distclean
+	git clean -xdf --exclude *.swp --exclude *.swo
+.PHONY: superclean
diff --git a/PackageInfo.g b/PackageInfo.g
index 882826f18..3b2edd693 100644
--- a/PackageInfo.g
+++ b/PackageInfo.g
@@ -209,8 +209,7 @@ Persons := [
     IsMaintainer  := false,
     PostalAddress := _STANDREWSCS,
     Email         := "obk1@st-andrews.ac.uk",
-    WWWHome       :=
-      "https://www.st-andrews.ac.uk/computer-science/people/obk1/",
+    WWWHome       := "https://olexandr-konovalov.github.io/",
     Place         := "St Andrews",
     Institution   := "University of St Andrews"),
 
diff --git a/autogen.sh b/autogen.sh
index e2fe78c5c..67bc0d8bd 100755
--- a/autogen.sh
+++ b/autogen.sh
@@ -1,2 +1,8 @@
 #!/bin/sh
-autoreconf -if `dirname "$0"`
+#
+# Regenerate configure from configure.ac. Requires GNU autoconf.
+set -ex
+mkdir -p gen
+aclocal -Wall --force
+autoconf -Wall -f
+autoheader -Wall -f
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index 5689cb0df..5dfe9596b 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -1,9 +1,9 @@
 pr:
-- master
+- main
 - stable-*.*
 
 trigger:
-- master
+- main
 - stable-*.*
 
 pool:
@@ -71,7 +71,7 @@ jobs:
     displayName: 'Running the Digraphs package for GAP tests in docker container. . .'
 - job: coverage
   variables:
-    SUITE: coverage 
+    SUITE: coverage
     ABI: 64
     GAP_VERSION: 4.11.0
     PACKAGES: latest
diff --git a/ci/docker-test.sh b/ci/docker-test.sh
index 0bbc1a668..d1f59d0c4 100755
--- a/ci/docker-test.sh
+++ b/ci/docker-test.sh
@@ -107,6 +107,11 @@ sudo chown -R gap: $GAP_HOME/pkg/digraphs
 
 bold "Compiling the Digraphs package..."
 cd "$GAP_HOME/pkg/digraphs"
+
+aclocal --version
+autoconf --version
+autoheader --version
+
 ./autogen.sh
 ./configure $PKG_FLAGS $EXTRA_PKG_FLAGS
 make
diff --git a/configure.ac b/configure.ac
index b742c0851..60f52a93a 100644
--- a/configure.ac
+++ b/configure.ac
@@ -9,25 +9,12 @@ dnl ##
 dnl ## Setup autoconf
 dnl ##
 AC_PREREQ([2.68])
-AC_INIT([digraphs], m4_esyscmd([tr -d '\n' < .VERSION]))
+AC_INIT([digraphs], [GAP package])
 AC_CONFIG_SRCDIR([src/digraphs.c])
-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
-
-dnl ##
-dnl ## Setup automake
-dnl ##
-AM_INIT_AUTOMAKE([1.11 -Wall foreign subdir-objects])
-AM_SILENT_RULES([yes])
-AM_PROG_AR
-
-AX_PREFIX_CONFIG_H([src/digraphs-config.h],[],[src/_pkgconfig.h])
+AX_PREFIX_CONFIG_H([src/digraphs-config.h],[digraphs],[gen/pkgconfig.h])
 
 AC_PREFIX_DEFAULT('${abs_top_builddir}/../../bin/')
 
@@ -38,26 +25,11 @@ AC_PROG_CC
 AC_PROG_CXX
 AC_LANG([C++])
 
-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 ##
 FIND_GAP
 
-dnl ##
-dnl ## Detect Windows resp. Cygwin
-dnl ##
-case $host_os in
-  *cygwin* ) CYGWIN=yes;;
-         * ) CYGWIN=no;;
-esac
-AM_CONDITIONAL([SYS_IS_CYGWIN], [test "$CYGWIN" = "yes"])
-
 dnl ## User setting: Debug mode (off by default)
 AC_ARG_ENABLE([debug],
     [AS_HELP_STRING([--enable-debug], [enable debug mode])],
@@ -66,8 +38,8 @@ 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])
+KERNEL_DEBUG=$enable_debug
+AC_SUBST(KERNEL_DEBUG)
 
 AC_ARG_ENABLE([stats],
     [AS_HELP_STRING([--enable-stats], [enable stats mode])],
@@ -76,10 +48,25 @@ AC_ARG_ENABLE([stats],
     )
 AC_MSG_CHECKING([whether to enable stats mode])
 AC_MSG_RESULT([$enable_stats])
+ENABLE_STATS=$enable_debug
+AC_SUBST(ENABLE_STATS)
+
+AC_ARG_ENABLE([code-coverage],
+  AS_HELP_STRING([--enable-code-coverage],
+  [Whether to enable code coverage support]),,
+  enable_code_coverage=no)
+AC_MSG_CHECKING([whether to build with code coverage support])
+AC_MSG_RESULT($enable_code_coverage)
+
+AS_IF([ test "$enable_code_coverage" = "yes" ], [
+    CODE_COVERAGE_CFLAGS="-DNDEBUG -O0 -g --coverage"
+    CODE_COVERAGE_CXXFLAGS="-DNDEBUG -O0 -g --coverage"
+    CODE_COVERAGE_LDFLAGS="--coverage"
+    AC_SUBST([CODE_COVERAGE_CFLAGS])
+    AC_SUBST([CODE_COVERAGE_CXXFLAGS])
+    AC_SUBST([CODE_COVERAGE_LDFLAGS])
+])
 
-AM_CONDITIONAL([ENABLE_STATS], [test "x$enable_stats" = xyes])
-
-AX_CODE_COVERAGE()
 
 # Enable compiler warnings 
 
@@ -106,17 +93,14 @@ AS_IF([test "x$enable_compile_warnings" != "xno"],
 
 # Check for system planarity suite
 
-AX_CHECK_PLANARITY()
-
+AX_CHECK_PLANARITY
 if test "x$with_external_planarity" = xno ; then
-  AC_CONFIG_SUBDIRS([extern/edge-addition-planarity-suite-Version_3.0.1.0])
   PLANARITY_SUITE_DIR=extern/edge-addition-planarity-suite-Version_3.0.1.0
   AC_SUBST(PLANARITY_SUITE_DIR)
 fi
 
 # Check for system bliss suite
-
-AX_CHECK_BLISS()
+AX_CHECK_BLISS
 
 # Check whether to use -mpopcnt and __builtin_ctzl
 AC_ARG_WITH([intrinsics],
diff --git a/m4/ax_append_compile_flags.m4 b/m4/ax_append_compile_flags.m4
index 5b6f1af51..9c856356c 100644
--- a/m4/ax_append_compile_flags.m4
+++ b/m4/ax_append_compile_flags.m4
@@ -30,33 +30,12 @@
 #
 #   Copyright (c) 2011 Maarten Bosmans <mkbosmans@gmail.com>
 #
-#   This program is free software: you can redistribute it and/or modify it
-#   under the terms of the GNU General Public License as published by the
-#   Free Software Foundation, either version 3 of the License, or (at your
-#   option) any later version.
-#
-#   This program is distributed in the hope that it will be useful, but
-#   WITHOUT ANY WARRANTY; without even the implied warranty of
-#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
-#   Public License for more details.
-#
-#   You should have received a copy of the GNU General Public License along
-#   with this program. If not, see <https://www.gnu.org/licenses/>.
-#
-#   As a special exception, the respective Autoconf Macro's copyright owner
-#   gives unlimited permission to copy, distribute and modify the configure
-#   scripts that are the output of Autoconf when processing the Macro. You
-#   need not follow the terms of the GNU General Public License when using
-#   or distributing such scripts, even though portions of the text of the
-#   Macro appear in them. The GNU General Public License (GPL) does govern
-#   all other use of the material that constitutes the Autoconf Macro.
-#
-#   This special exception to the GPL applies to versions of the Autoconf
-#   Macro released by the Autoconf Archive. When you make and distribute a
-#   modified version of the Autoconf Macro, you may extend this special
-#   exception to the GPL to apply to your modified version as well.
+#   Copying and distribution of this file, with or without modification, are
+#   permitted in any medium without royalty provided the copyright notice
+#   and this notice are preserved.  This file is offered as-is, without any
+#   warranty.
 
-#serial 6
+#serial 7
 
 AC_DEFUN([AX_APPEND_COMPILE_FLAGS],
 [AX_REQUIRE_DEFINED([AX_CHECK_COMPILE_FLAG])
diff --git a/m4/ax_append_flag.m4 b/m4/ax_append_flag.m4
index e8c5312af..dd6d8b614 100644
--- a/m4/ax_append_flag.m4
+++ b/m4/ax_append_flag.m4
@@ -23,33 +23,12 @@
 #   Copyright (c) 2008 Guido U. Draheim <guidod@gmx.de>
 #   Copyright (c) 2011 Maarten Bosmans <mkbosmans@gmail.com>
 #
-#   This program is free software: you can redistribute it and/or modify it
-#   under the terms of the GNU General Public License as published by the
-#   Free Software Foundation, either version 3 of the License, or (at your
-#   option) any later version.
-#
-#   This program is distributed in the hope that it will be useful, but
-#   WITHOUT ANY WARRANTY; without even the implied warranty of
-#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
-#   Public License for more details.
-#
-#   You should have received a copy of the GNU General Public License along
-#   with this program. If not, see <https://www.gnu.org/licenses/>.
-#
-#   As a special exception, the respective Autoconf Macro's copyright owner
-#   gives unlimited permission to copy, distribute and modify the configure
-#   scripts that are the output of Autoconf when processing the Macro. You
-#   need not follow the terms of the GNU General Public License when using
-#   or distributing such scripts, even though portions of the text of the
-#   Macro appear in them. The GNU General Public License (GPL) does govern
-#   all other use of the material that constitutes the Autoconf Macro.
-#
-#   This special exception to the GPL applies to versions of the Autoconf
-#   Macro released by the Autoconf Archive. When you make and distribute a
-#   modified version of the Autoconf Macro, you may extend this special
-#   exception to the GPL to apply to your modified version as well.
+#   Copying and distribution of this file, with or without modification, are
+#   permitted in any medium without royalty provided the copyright notice
+#   and this notice are preserved.  This file is offered as-is, without any
+#   warranty.
 
-#serial 7
+#serial 8
 
 AC_DEFUN([AX_APPEND_FLAG],
 [dnl
diff --git a/m4/ax_check_bliss.m4 b/m4/ax_check_bliss.m4
index b73524b0e..b418072a2 100644
--- a/m4/ax_check_bliss.m4
+++ b/m4/ax_check_bliss.m4
@@ -24,8 +24,9 @@ AC_DEFUN([AX_CHECK_BLISS], [
                         [AC_MSG_ERROR([no external bliss headers found])])
         AC_LANG_POP()
   fi
-  AM_CONDITIONAL([WITH_INCLUDED_BLISS], [test "x$with_external_bliss" = xno])
   if test "x$with_external_bliss" = xno ; then
+    WITH_INCLUDED_BLISS=yes
+    AC_SUBST(WITH_INCLUDED_BLISS)
     AC_DEFINE([WITH_INCLUDED_BLISS],
               [1],
               [define that we should use the vendored bliss])
diff --git a/m4/ax_check_planarity.m4 b/m4/ax_check_planarity.m4
index e18bbb5cb..2d44c9068 100644
--- a/m4/ax_check_planarity.m4
+++ b/m4/ax_check_planarity.m4
@@ -24,8 +24,9 @@ AC_DEFUN([AX_CHECK_PLANARITY], [
                         [AC_MSG_ERROR([no external planarity headers found])])
         AC_LANG_POP()
   fi
-  AM_CONDITIONAL([WITH_INCLUDED_PLANARITY], [test "x$with_external_planarity" = xno])
   if test "x$with_external_planarity" = xno ; then
+    WITH_INCLUDED_PLANARITY=yes
+    AC_SUBST(WITH_INCLUDED_PLANARITY)
     AC_DEFINE([WITH_INCLUDED_PLANARITY], 
               [1], 
               [define that we should use the vendored planarity])
diff --git a/m4/ax_code_coverage.m4 b/m4/ax_code_coverage.m4
deleted file mode 100644
index 6484f0332..000000000
--- a/m4/ax_code_coverage.m4
+++ /dev/null
@@ -1,264 +0,0 @@
-# ===========================================================================
-#     https://www.gnu.org/software/autoconf-archive/ax_code_coverage.html
-# ===========================================================================
-#
-# SYNOPSIS
-#
-#   AX_CODE_COVERAGE()
-#
-# DESCRIPTION
-#
-#   Defines CODE_COVERAGE_CPPFLAGS, CODE_COVERAGE_CFLAGS,
-#   CODE_COVERAGE_CXXFLAGS and CODE_COVERAGE_LIBS which should be included
-#   in the CPPFLAGS, CFLAGS CXXFLAGS and LIBS/LIBADD variables of every
-#   build target (program or library) which should be built with code
-#   coverage support. Also defines CODE_COVERAGE_RULES which should be
-#   substituted in your Makefile; and $enable_code_coverage which can be
-#   used in subsequent configure output. CODE_COVERAGE_ENABLED is defined
-#   and substituted, and corresponds to the value of the
-#   --enable-code-coverage option, which defaults to being disabled.
-#
-#   Test also for gcov program and create GCOV variable that could be
-#   substituted.
-#
-#   Note that all optimization flags in CFLAGS must be disabled when code
-#   coverage is enabled.
-#
-#   Usage example:
-#
-#   configure.ac:
-#
-#     AX_CODE_COVERAGE
-#
-#   Makefile.am:
-#
-#     @CODE_COVERAGE_RULES@
-#     my_program_LIBS = ... $(CODE_COVERAGE_LIBS) ...
-#     my_program_CPPFLAGS = ... $(CODE_COVERAGE_CPPFLAGS) ...
-#     my_program_CFLAGS = ... $(CODE_COVERAGE_CFLAGS) ...
-#     my_program_CXXFLAGS = ... $(CODE_COVERAGE_CXXFLAGS) ...
-#
-#   This results in a "check-code-coverage" rule being added to any
-#   Makefile.am which includes "@CODE_COVERAGE_RULES@" (assuming the module
-#   has been configured with --enable-code-coverage). Running `make
-#   check-code-coverage` in that directory will run the module's test suite
-#   (`make check`) and build a code coverage report detailing the code which
-#   was touched, then print the URI for the report.
-#
-#   In earlier versions of this macro, CODE_COVERAGE_LDFLAGS was defined
-#   instead of CODE_COVERAGE_LIBS. They are both still defined, but use of
-#   CODE_COVERAGE_LIBS is preferred for clarity; CODE_COVERAGE_LDFLAGS is
-#   deprecated. They have the same value.
-#
-#   This code was derived from Makefile.decl in GLib, originally licenced
-#   under LGPLv2.1+.
-#
-# LICENSE
-#
-#   Copyright (c) 2012, 2016 Philip Withnall
-#   Copyright (c) 2012 Xan Lopez
-#   Copyright (c) 2012 Christian Persch
-#   Copyright (c) 2012 Paolo Borelli
-#   Copyright (c) 2012 Dan Winship
-#   Copyright (c) 2015 Bastien ROUCARIES
-#
-#   This library is free software; you can redistribute it and/or modify it
-#   under the terms of the GNU Lesser General Public License as published by
-#   the Free Software Foundation; either version 2.1 of the License, or (at
-#   your option) any later version.
-#
-#   This library is distributed in the hope that it will be useful, but
-#   WITHOUT ANY WARRANTY; without even the implied warranty of
-#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser
-#   General Public License for more details.
-#
-#   You should have received a copy of the GNU Lesser General Public License
-#   along with this program. If not, see <https://www.gnu.org/licenses/>.
-
-#serial 25
-
-AC_DEFUN([AX_CODE_COVERAGE],[
-	dnl Check for --enable-code-coverage
-	AC_REQUIRE([AC_PROG_SED])
-
-	# allow to override gcov location
-	AC_ARG_WITH([gcov],
-	  [AS_HELP_STRING([--with-gcov[=GCOV]], [use given GCOV for coverage (GCOV=gcov).])],
-	  [_AX_CODE_COVERAGE_GCOV_PROG_WITH=$with_gcov],
-	  [_AX_CODE_COVERAGE_GCOV_PROG_WITH=gcov])
-
-	AC_MSG_CHECKING([whether to build with code coverage support])
-	AC_ARG_ENABLE([code-coverage],
-	  AS_HELP_STRING([--enable-code-coverage],
-	  [Whether to enable code coverage support]),,
-	  enable_code_coverage=no)
-
-	AM_CONDITIONAL([CODE_COVERAGE_ENABLED], [test x$enable_code_coverage = xyes])
-	AC_SUBST([CODE_COVERAGE_ENABLED], [$enable_code_coverage])
-	AC_MSG_RESULT($enable_code_coverage)
-
-	AS_IF([ test "$enable_code_coverage" = "yes" ], [
-		# check for gcov
-		AC_CHECK_TOOL([GCOV],
-		  [$_AX_CODE_COVERAGE_GCOV_PROG_WITH],
-		  [:])
-		AS_IF([test "X$GCOV" = "X:"],
-		  [AC_MSG_ERROR([gcov is needed to do coverage])])
-		AC_SUBST([GCOV])
-
-		dnl Check if gcc is being used
-		AS_IF([ test "$GCC" = "no" ], [
-			AC_MSG_ERROR([not compiling with gcc, which is required for gcov code coverage])
-		])
-
-		AC_CHECK_PROG([LCOV], [lcov], [lcov])
-		AC_CHECK_PROG([GENHTML], [genhtml], [genhtml])
-
-		AS_IF([ test -z "$LCOV" ], [
-			AC_MSG_ERROR([To enable code coverage reporting you must have lcov installed])
-		])
-
-		AS_IF([ test -z "$GENHTML" ], [
-			AC_MSG_ERROR([Could not find genhtml from the lcov package])
-		])
-
-		dnl Build the code coverage flags
-		dnl Define CODE_COVERAGE_LDFLAGS for backwards compatibility
-		CODE_COVERAGE_CPPFLAGS="-DNDEBUG"
-		CODE_COVERAGE_CFLAGS="-O0 -g -fprofile-arcs -ftest-coverage"
-		CODE_COVERAGE_CXXFLAGS="-O0 -g -fprofile-arcs -ftest-coverage"
-		CODE_COVERAGE_LIBS="-lgcov"
-		CODE_COVERAGE_LDFLAGS="$CODE_COVERAGE_LIBS"
-
-		AC_SUBST([CODE_COVERAGE_CPPFLAGS])
-		AC_SUBST([CODE_COVERAGE_CFLAGS])
-		AC_SUBST([CODE_COVERAGE_CXXFLAGS])
-		AC_SUBST([CODE_COVERAGE_LIBS])
-		AC_SUBST([CODE_COVERAGE_LDFLAGS])
-
-		[CODE_COVERAGE_RULES_CHECK='
-	-$(A''M_V_at)$(MAKE) $(AM_MAKEFLAGS) -k check
-	$(A''M_V_at)$(MAKE) $(AM_MAKEFLAGS) code-coverage-capture
-']
-		[CODE_COVERAGE_RULES_CAPTURE='
-	$(code_coverage_v_lcov_cap)$(LCOV) $(code_coverage_quiet) $(addprefix --directory ,$(CODE_COVERAGE_DIRECTORY)) --capture --output-file "$(CODE_COVERAGE_OUTPUT_FILE).tmp" --test-name "$(call code_coverage_sanitize,$(PACKAGE_NAME)-$(PACKAGE_VERSION))" --no-checksum --compat-libtool $(CODE_COVERAGE_LCOV_SHOPTS) $(CODE_COVERAGE_LCOV_OPTIONS)
-	$(code_coverage_v_lcov_ign)$(LCOV) $(code_coverage_quiet) $(addprefix --directory ,$(CODE_COVERAGE_DIRECTORY)) --remove "$(CODE_COVERAGE_OUTPUT_FILE).tmp" "/tmp/*" $(CODE_COVERAGE_IGNORE_PATTERN) --output-file "$(CODE_COVERAGE_OUTPUT_FILE)" $(CODE_COVERAGE_LCOV_SHOPTS) $(CODE_COVERAGE_LCOV_RMOPTS)
-	-@rm -f $(CODE_COVERAGE_OUTPUT_FILE).tmp
-	$(code_coverage_v_genhtml)LANG=C $(GENHTML) $(code_coverage_quiet) $(addprefix --prefix ,$(CODE_COVERAGE_DIRECTORY)) --output-directory "$(CODE_COVERAGE_OUTPUT_DIRECTORY)" --title "$(PACKAGE_NAME)-$(PACKAGE_VERSION) Code Coverage" --legend --show-details "$(CODE_COVERAGE_OUTPUT_FILE)" $(CODE_COVERAGE_GENHTML_OPTIONS)
-	@echo "file://$(abs_builddir)/$(CODE_COVERAGE_OUTPUT_DIRECTORY)/index.html"
-']
-		[CODE_COVERAGE_RULES_CLEAN='
-clean: code-coverage-clean
-distclean: code-coverage-clean
-code-coverage-clean:
-	-$(LCOV) --directory $(top_builddir) -z
-	-rm -rf $(CODE_COVERAGE_OUTPUT_FILE) $(CODE_COVERAGE_OUTPUT_FILE).tmp $(CODE_COVERAGE_OUTPUT_DIRECTORY)
-	-find . \( -name "*.gcda" -o -name "*.gcno" -o -name "*.gcov" \) -delete
-']
-	], [
-		[CODE_COVERAGE_RULES_CHECK='
-	@echo "Need to reconfigure with --enable-code-coverage"
-']
-		CODE_COVERAGE_RULES_CAPTURE="$CODE_COVERAGE_RULES_CHECK"
-		CODE_COVERAGE_RULES_CLEAN=''
-	])
-
-[CODE_COVERAGE_RULES='
-# Code coverage
-#
-# Optional:
-#  - CODE_COVERAGE_DIRECTORY: Top-level directory for code coverage reporting.
-#    Multiple directories may be specified, separated by whitespace.
-#    (Default: $(top_builddir))
-#  - CODE_COVERAGE_OUTPUT_FILE: Filename and path for the .info file generated
-#    by lcov for code coverage. (Default:
-#    $(PACKAGE_NAME)-$(PACKAGE_VERSION)-coverage.info)
-#  - CODE_COVERAGE_OUTPUT_DIRECTORY: Directory for generated code coverage
-#    reports to be created. (Default:
-#    $(PACKAGE_NAME)-$(PACKAGE_VERSION)-coverage)
-#  - CODE_COVERAGE_BRANCH_COVERAGE: Set to 1 to enforce branch coverage,
-#    set to 0 to disable it and leave empty to stay with the default.
-#    (Default: empty)
-#  - CODE_COVERAGE_LCOV_SHOPTS_DEFAULT: Extra options shared between both lcov
-#    instances. (Default: based on $CODE_COVERAGE_BRANCH_COVERAGE)
-#  - CODE_COVERAGE_LCOV_SHOPTS: Extra options to shared between both lcov
-#    instances. (Default: $CODE_COVERAGE_LCOV_SHOPTS_DEFAULT)
-#  - CODE_COVERAGE_LCOV_OPTIONS_GCOVPATH: --gcov-tool pathtogcov
-#  - CODE_COVERAGE_LCOV_OPTIONS_DEFAULT: Extra options to pass to the
-#    collecting lcov instance. (Default: $CODE_COVERAGE_LCOV_OPTIONS_GCOVPATH)
-#  - CODE_COVERAGE_LCOV_OPTIONS: Extra options to pass to the collecting lcov
-#    instance. (Default: $CODE_COVERAGE_LCOV_OPTIONS_DEFAULT)
-#  - CODE_COVERAGE_LCOV_RMOPTS_DEFAULT: Extra options to pass to the filtering
-#    lcov instance. (Default: empty)
-#  - CODE_COVERAGE_LCOV_RMOPTS: Extra options to pass to the filtering lcov
-#    instance. (Default: $CODE_COVERAGE_LCOV_RMOPTS_DEFAULT)
-#  - CODE_COVERAGE_GENHTML_OPTIONS_DEFAULT: Extra options to pass to the
-#    genhtml instance. (Default: based on $CODE_COVERAGE_BRANCH_COVERAGE)
-#  - CODE_COVERAGE_GENHTML_OPTIONS: Extra options to pass to the genhtml
-#    instance. (Default: $CODE_COVERAGE_GENHTML_OPTIONS_DEFAULT)
-#  - CODE_COVERAGE_IGNORE_PATTERN: Extra glob pattern of files to ignore
-#
-# The generated report will be titled using the $(PACKAGE_NAME) and
-# $(PACKAGE_VERSION). In order to add the current git hash to the title,
-# use the git-version-gen script, available online.
-
-# Optional variables
-CODE_COVERAGE_DIRECTORY ?= $(top_builddir)
-CODE_COVERAGE_OUTPUT_FILE ?= $(PACKAGE_NAME)-$(PACKAGE_VERSION)-coverage.info
-CODE_COVERAGE_OUTPUT_DIRECTORY ?= $(PACKAGE_NAME)-$(PACKAGE_VERSION)-coverage
-CODE_COVERAGE_BRANCH_COVERAGE ?=
-CODE_COVERAGE_LCOV_SHOPTS_DEFAULT ?= $(if $(CODE_COVERAGE_BRANCH_COVERAGE),\
---rc lcov_branch_coverage=$(CODE_COVERAGE_BRANCH_COVERAGE))
-CODE_COVERAGE_LCOV_SHOPTS ?= $(CODE_COVERAGE_LCOV_SHOPTS_DEFAULT)
-CODE_COVERAGE_LCOV_OPTIONS_GCOVPATH ?= --gcov-tool "$(GCOV)"
-CODE_COVERAGE_LCOV_OPTIONS_DEFAULT ?= $(CODE_COVERAGE_LCOV_OPTIONS_GCOVPATH)
-CODE_COVERAGE_LCOV_OPTIONS ?= $(CODE_COVERAGE_LCOV_OPTIONS_DEFAULT)
-CODE_COVERAGE_LCOV_RMOPTS_DEFAULT ?=
-CODE_COVERAGE_LCOV_RMOPTS ?= $(CODE_COVERAGE_LCOV_RMOPTS_DEFAULT)
-CODE_COVERAGE_GENHTML_OPTIONS_DEFAULT ?=\
-$(if $(CODE_COVERAGE_BRANCH_COVERAGE),\
---rc genhtml_branch_coverage=$(CODE_COVERAGE_BRANCH_COVERAGE))
-CODE_COVERAGE_GENHTML_OPTIONS ?= $(CODE_COVERAGE_GENHTML_OPTIONS_DEFAULT)
-CODE_COVERAGE_IGNORE_PATTERN ?=
-
-GITIGNOREFILES ?=
-GITIGNOREFILES += $(CODE_COVERAGE_OUTPUT_FILE) $(CODE_COVERAGE_OUTPUT_DIRECTORY)
-
-code_coverage_v_lcov_cap = $(code_coverage_v_lcov_cap_$(V))
-code_coverage_v_lcov_cap_ = $(code_coverage_v_lcov_cap_$(AM_DEFAULT_VERBOSITY))
-code_coverage_v_lcov_cap_0 = @echo "  LCOV   --capture"\
- $(CODE_COVERAGE_OUTPUT_FILE);
-code_coverage_v_lcov_ign = $(code_coverage_v_lcov_ign_$(V))
-code_coverage_v_lcov_ign_ = $(code_coverage_v_lcov_ign_$(AM_DEFAULT_VERBOSITY))
-code_coverage_v_lcov_ign_0 = @echo "  LCOV   --remove /tmp/*"\
- $(CODE_COVERAGE_IGNORE_PATTERN);
-code_coverage_v_genhtml = $(code_coverage_v_genhtml_$(V))
-code_coverage_v_genhtml_ = $(code_coverage_v_genhtml_$(AM_DEFAULT_VERBOSITY))
-code_coverage_v_genhtml_0 = @echo "  GEN   " $(CODE_COVERAGE_OUTPUT_DIRECTORY);
-code_coverage_quiet = $(code_coverage_quiet_$(V))
-code_coverage_quiet_ = $(code_coverage_quiet_$(AM_DEFAULT_VERBOSITY))
-code_coverage_quiet_0 = --quiet
-
-# sanitizes the test-name: replaces with underscores: dashes and dots
-code_coverage_sanitize = $(subst -,_,$(subst .,_,$(1)))
-
-# Use recursive makes in order to ignore errors during check
-check-code-coverage:'"$CODE_COVERAGE_RULES_CHECK"'
-
-# Capture code coverage data
-code-coverage-capture: code-coverage-capture-hook'"$CODE_COVERAGE_RULES_CAPTURE"'
-
-# Hook rule executed before code-coverage-capture, overridable by the user
-code-coverage-capture-hook:
-
-'"$CODE_COVERAGE_RULES_CLEAN"'
-
-A''M_DISTCHECK_CONFIGURE_FLAGS ?=
-A''M_DISTCHECK_CONFIGURE_FLAGS += --disable-code-coverage
-
-.PHONY: check-code-coverage code-coverage-capture code-coverage-capture-hook code-coverage-clean
-']
-
-	AC_SUBST([CODE_COVERAGE_RULES])
-	m4_ifdef([_AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE([CODE_COVERAGE_RULES])])
-])
diff --git a/src/CPPLINT.cfg b/src/CPPLINT.cfg
index ebe3d5303..5409d4c1e 100644
--- a/src/CPPLINT.cfg
+++ b/src/CPPLINT.cfg
@@ -2,4 +2,4 @@ set noparent
 filter=-build/include_subdir,-runtime/indentation_namespace,-runtime/references, -readability/casting,-runtime/threadsafe_fn,-runtime/int,-readability/todo
 linelength=80
 root=../..
-exclude_files=(_pkgconfig.h|digraphs-config.h)
+exclude_files=(pkgconfig.h|digraphs-config.h)
diff --git a/src/cliques.c b/src/cliques.c
index abb86907c..487608df9 100644
--- a/src/cliques.c
+++ b/src/cliques.c
@@ -6,7 +6,7 @@
 //
 // This file is free software, see the digraphs/LICENSE.
 
-#include <cliques.h>
+#include "cliques.h"
 
 // C headers
 #include <stdbool.h>  // for true, false, bool