diff --git a/.gitignore b/.gitignore
index 32cd6bc..b3f78a7 100644
--- a/.gitignore
+++ b/.gitignore
@@ -21,7 +21,6 @@ libtool
 ltmain.sh
 m4/
 Makefile
-Makefile.am
 Makefile.in
 missing
 NEWS
diff --git a/Makefile.am b/Makefile.am
new file mode 100644
index 0000000..4e70694
--- /dev/null
+++ b/Makefile.am
@@ -0,0 +1,15 @@
+AUTOMAKE_OPTIONS = subdir-objects
+ACLOCAL_AMFLAGS = -I m4
+
+dist_man_MANS = man/ccr.1
+dist_noinst_SCRIPTS = autogen.sh
+bin_PROGRAMS = ccr
+
+ccr_SOURCES = src/hash.cpp src/sencode.cpp src/gf2m.cpp src/chacha.cpp src/algo_suite.cpp src/fft.cpp src/hashfile.cpp src/symkey.cpp src/bvector.cpp src/str_match.cpp src/keyring.cpp src/ios.cpp src/algos_enc.cpp src/message.cpp src/sc.cpp src/envelope.cpp src/permutation.cpp src/mce_qcmdpc.cpp src/pwrng.cpp src/xsynd.cpp src/serialization.cpp src/generator.cpp src/iohelpers.cpp src/main.cpp src/actions.cpp src/polynomial.cpp src/algos_sig.cpp src/matrix.cpp src/seclock.cpp src/base64.cpp src/privfile.cpp src/fmtseq.cpp
+noinst_HEADERS = src/str_match.h src/permutation.h src/rmd_hash.h src/fft.h src/mce_qcmdpc.h src/hash.h src/algo_suite.h src/message.h src/symkey.h src/polynomial.h src/gf2m.h src/factoryof.h src/keyring.h src/sc.h src/fmtseq.h src/cube_hash.h src/xsynd.h src/arcfour.h src/sencode.h src/sha_hash.h src/prng.h src/tiger_hash.h src/generator.h src/decoding.h src/iohelpers.h src/cubehash_impl.h src/algorithm.h src/ios.h src/bvector.h src/hashfile.h src/actions.h src/types.h src/pwrng.h src/algos_sig.h src/matrix.h src/chacha.h src/algos_enc.h src/privfile.h src/vector_item.h src/base64.h src/envelope.h src/seclock.h
+
+AM_CPPFLAGS = -I$(top_srcdir)
+AM_CFLAGS = -Wall
+
+ccr_CPPFLAGS = $(FFTW3_CFLAGS) $(CRYPTOPP_CFLAGS)
+ccr_LDADD = $(FFTW3_LIBS) $(CRYPTOPP_LIBS)
diff --git a/configure.ac b/configure.ac
index e2c1e5d..dc0ca09 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,85 +1,70 @@
-
-AC_PREREQ(2.6)
+AC_PREREQ([2.69])
 AC_INIT([codecrypt], [1.8])
-AC_CONFIG_AUX_DIR(.) # because of libtoolize
+AC_CONFIG_AUX_DIR([build-aux]) dnl because of libtoolize
 AC_CONFIG_MACRO_DIR([m4])
 
 AM_INIT_AUTOMAKE()
-m4_ifdef([AM_SILENT_RULES],[AM_SILENT_RULES([yes])])
-
-CFLAGS="$CFLAGS"
-CXXFLAGS="$CXXFLAGS"
-LDFLAGS="$LDFLAGS"
+m4_ifdef([AM_SILENT_RULES], [AM_SILENT_RULES([yes])])
 
 LT_INIT
-
-AM_PROG_CC_C_O
 AC_PROG_CXX
-AC_PROG_CPP
-AC_PROG_INSTALL
 
-#check for compilable GMP presence
-AC_CHECK_HEADERS([gmp.h], , AC_MSG_ERROR([Codecrypt requires gmp.h]))
-AC_CHECK_LIB(gmp, __gmpz_init, , AC_MSG_ERROR([Codecrypt requires libgmp]))
+dnl check for compilable GMP presence
+AC_CHECK_HEADERS([gmp.h], [], [AC_MSG_ERROR([Codecrypt requires gmp.h])])
+AC_SEARCH_LIBS([__gmpz_init], [gmp], [], [AC_MSG_ERROR([Codecrypt requires libgmp])])
 
-#check for FFTW library presence
-AC_CHECK_HEADERS([fftw3.h], , AC_MSG_ERROR([Codecrypt requires fftw3.h]))
-AC_CHECK_LIB(fftw3, fftw_plan_dft_1d, , AC_MSG_ERROR([Codecrypt requires libfftw3]))
+dnl check for FFTW library presence
+PKG_CHECK_MODULES([FFTW3], [fftw3])
 
-#check whether to build with crypto++
+dnl check whether to build with crypto++
 AC_ARG_WITH([cryptopp],
-	AC_HELP_STRING([--with-cryptopp],[Build algorithms that need Crypto++ support]),
-	[WITH_CRYPTOPP=$withval],
-	[WITH_CRYPTOPP=yes])
+    [AS_HELP_STRING([--with-cryptopp], [Build algorithms that need Crypto++ support])])
 
-#and check crypto++
-if test "$WITH_CRYPTOPP" = "yes"; then
-	
-	PKG_PROG_PKG_CONFIG([0.25])
+dnl and check crypto++
+AS_IF([test "x$with_cryptopp" != "xno"], [
+    PKG_PROG_PKG_CONFIG([0.25])
 
-	PKG_CHECK_MODULES([CRYPTOPP],[libcrypto++])
+    PKG_CHECK_MODULES([CRYPTOPP], [libcrypto++], [], [
+        AC_MSG_CHECKING([for libcrypto++ using known flags])
+        AC_LANG_PUSH([C++])
+        saved_LIBS="$LIBS"
+        LIBS+=" -lcrypto++"
+        AC_LINK_IFELSE([
+            AC_LANG_PROGRAM([#include <crypto++/cryptlib.h>], [CryptoPP::NullRNG])], [
+                CRYPTOPP_LIBS="-lcrypto++"
+                AC_MSG_RESULT([${CRYPTOPP_LIBS}])
+            ], [
+                AC_MSG_ERROR([Cannot find crypto++])
+            ])
+        LIBS="$saved_LIBS"
+        AC_LANG_POP([C++])
+    ])
 
-	#crypto++ headers are either in include/crypto++ or include/cryptopp,
-	#the information is otherwise unavailable from standard configuration
-	#means. Please report/add more tests if you encounter distros that
-	#place them elsewhere.
-	AC_LANG_PUSH([C++])
-	AC_CHECK_HEADER([crypto++/config.h],
-		AC_DEFINE([CRYPTOPP_DIR_PLUS], [1]),
-		AC_DEFINE([CRYPTOPP_DIR_PLUS], [0])
-	)
-	AC_LANG_POP([C++])
+    AC_DEFINE([HAVE_CRYPTOPP], [1], [Enable support for crypto++ routines])
+], [
+    AC_DEFINE([HAVE_CRYPTOPP], [0], [Enable support for crypto++ routines])
+])
 
-	AC_DEFINE([HAVE_CRYPTOPP], [1])
-else
-	AC_DEFINE([HAVE_CRYPTOPP], [0])
-fi
-
-#check for readpassphrase. If none is found, we use getpass (with a warning)
+dnl check for readpassphrase. If none is found, we use getpass (with a warning)
 AC_CHECK_HEADER([readpassphrase.h],
-	[READPASSPHRASE=native],
-	AC_CHECK_HEADER([bsd/readpassphrase.h],
-		[READPASSPHRASE=bsd], ))
+    [READPASSPHRASE=native],
+    AC_CHECK_HEADER([bsd/readpassphrase.h],
+        [READPASSPHRASE=bsd], []))
 
-if test "$READPASSPHRASE" = "native"; then
-	AC_DEFINE([HAVE_READPASSPHRASE], [1])
-fi
-if test "$READPASSPHRASE" = "bsd"; then
-	AC_DEFINE([HAVE_BSDREADPASSPHRASE], [1])
-	AC_CHECK_LIB([bsd], [readpassphrase],
-		[LIBS="-lbsd $LIBS"], #is there a better version of this?
-		AC_MSG_ERROR([library for bsd/readpassphrase.h not found]))
-fi
+AS_IF([test "x$READPASSPHRASE" = "xnative"],[
+    AC_DEFINE([HAVE_READPASSPHRASE], [1], [Enable readpassphrase])])
 
-#check for standard functions
-AC_CHECK_FUNCS([memset mkdir], , AC_MSG_ERROR([Required function missing]))
+AS_IF([test "x$READPASSPHRASE" = "xbsd"],[
+    AC_DEFINE([HAVE_BSDREADPASSPHRASE], [1], [Enable bsdreadpassphrase])
+    AC_SEARCH_LIBS([readpassphrase], [bsd], [], [AC_MSG_ERROR([library for bsd/readpassphrase.h not found])])])
 
-#unixy headers
-AC_CHECK_HEADERS([fcntl.h inttypes.h stddef.h stdlib.h string.h sys/file.h unistd.h], , AC_MSG_ERROR([Required header file missing]))
+dnl check for standard functions
+AC_CHECK_FUNCS([memset mkdir], [], [AC_MSG_ERROR([Required function missing])])
 
-#other used stuff
-AC_CHECK_HEADER_STDBOOL
-AC_C_INLINE
+dnl POSIX headers
+AC_CHECK_HEADERS([fcntl.h inttypes.h stddef.h stdlib.h string.h sys/file.h unistd.h], [], [AC_MSG_ERROR([Required header file missing])])
+
+dnl other used stuff
 AC_TYPE_SIZE_T
 AC_TYPE_SSIZE_T
 AC_TYPE_UINT32_T