diff --git a/autogen.sh b/autogen.sh
index 5c2b866edb..568e47f29c 100755
--- a/autogen.sh
+++ b/autogen.sh
@@ -30,7 +30,7 @@ fi
 
 echo "Processing configure.ac"
 
-autoreconf --force --install --verbose
+(cd $srcdir; autoreconf --install --verbose)
 
 if [ "$NOCONFIGURE" = 1 ]; then
     echo "Done. configure skipped."
diff --git a/configure.ac b/configure.ac
index 39636c8825..10d19a1276 100644
--- a/configure.ac
+++ b/configure.ac
@@ -9,6 +9,10 @@ AC_CONFIG_MACRO_DIR([m4])
 AM_INIT_AUTOMAKE([1.11 -Wall parallel-tests subdir-objects])
 AC_CONFIG_HEADERS([config.h])
 
+# Silence "AC_LINK_IFELSE before AC_USE_SYSTEM_EXTENSIONS" warnings
+# Note: Enables _GNU_SOURCE on Linux
+AC_USE_SYSTEM_EXTENSIONS
+
 AM_GNU_GETTEXT_VERSION([0.19.8])
 AM_GNU_GETTEXT([external])
 
@@ -23,15 +27,10 @@ if test -n "${build}" -a -n "${target}"; then
 	GEANY_STATUS_ADD([Building Geany for], [${target}])
 fi
 
-# why do we use this?
-AC_USE_SYSTEM_EXTENSIONS
-
 m4_ifdef([AM_PROG_AR],[AM_PROG_AR])
 LT_INIT([disable-static])
 AC_PROG_CC
-AC_PROG_CC_C99
 AM_PROG_CC_C_O
-
 AC_PROG_CXX
 GEANY_PROG_CXX
 AX_CXX_COMPILE_STDCXX_17
@@ -39,6 +38,10 @@ AX_CXX_COMPILE_STDCXX_17
 AC_PROG_INSTALL
 AC_PROG_LN_S
 
+if test "$ac_cv_prog_cc_c99" = "no"; then
+	AC_MSG_ERROR([Need a C99 compiler])
+fi
+
 # autoscan start
 
 # Checks for header files.
diff --git a/m4/geany-plugins.m4 b/m4/geany-plugins.m4
index adf60f497c..665003dc43 100644
--- a/m4/geany-plugins.m4
+++ b/m4/geany-plugins.m4
@@ -5,7 +5,7 @@ dnl Result is available in the geany_enable_plugins variable
 AC_DEFUN([GEANY_CHECK_PLUGINS],
 [
 	AC_REQUIRE([AC_DISABLE_STATIC])
-	AC_REQUIRE([AM_PROG_LIBTOOL])
+	AC_REQUIRE([LT_INIT])
 
 	AC_ARG_ENABLE([plugins],
 			[AS_HELP_STRING([--disable-plugins], [compile without plugin support [default=no]])],