diff --git a/Makefile.am b/Makefile.am
index 76652ce5..eefeca22 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -2,83 +2,83 @@ bin_PROGRAMS = snapraid
 check_PROGRAMS = mktest
 
 snapraid_SOURCES = \
-	src/raid/raid.c \
-	src/raid/module.c \
-	src/raid/tables.c \
-	src/raid/int.c \
-	src/raid/x86.c \
-	src/raid/intz.c \
-	src/raid/x86z.c \
-	src/raid/helper.c \
-	src/raid/memory.c \
-	src/raid/test.c \
-	src/raid/tag.c \
-	src/tommyds/tommy.c \
-	src/snapraid.c \
-	src/util.c \
-	src/elem.c \
-	src/state.c \
-	src/scan.c \
-	src/sync.c \
-	src/check.c \
-	src/dry.c \
-	src/rehash.c \
-	src/scrub.c \
-	src/status.c \
-	src/dup.c \
-	src/list.c \
-	src/pool.c \
-	src/parity.c \
-	src/handle.c \
-	src/fnmatch.c \
-	src/selftest.c \
-	src/speed.c \
-	src/import.c \
-	src/mingw.c \
-	src/unix.c
+	raid/raid.c \
+	raid/module.c \
+	raid/tables.c \
+	raid/int.c \
+	raid/x86.c \
+	raid/intz.c \
+	raid/x86z.c \
+	raid/helper.c \
+	raid/memory.c \
+	raid/test.c \
+	raid/tag.c \
+	tommyds/tommy.c \
+	cmdline/snapraid.c \
+	cmdline/util.c \
+	cmdline/elem.c \
+	cmdline/state.c \
+	cmdline/scan.c \
+	cmdline/sync.c \
+	cmdline/check.c \
+	cmdline/dry.c \
+	cmdline/rehash.c \
+	cmdline/scrub.c \
+	cmdline/status.c \
+	cmdline/dup.c \
+	cmdline/list.c \
+	cmdline/pool.c \
+	cmdline/parity.c \
+	cmdline/handle.c \
+	cmdline/fnmatch.c \
+	cmdline/selftest.c \
+	cmdline/speed.c \
+	cmdline/import.c \
+	cmdline/mingw.c \
+	cmdline/unix.c
 
 noinst_HEADERS = \
-	src/raid/raid.h \
-	src/raid/helper.h \
-	src/raid/internal.h \
-	src/raid/cpu.h \
-	src/raid/gf.h \
-	src/raid/combo.h \
-	src/raid/memory.h \
-	src/raid/test.h \
-	src/tommyds/tommyarray.h \
-	src/tommyds/tommyarrayblk.h \
-	src/tommyds/tommyarrayblkof.h \
-	src/tommyds/tommychain.h \
-	src/tommyds/tommyhash.h \
-	src/tommyds/tommyhashdyn.h \
-	src/tommyds/tommylist.h \
-	src/tommyds/tommytypes.h \
-	src/tommyds/tommyarray.c \
-	src/tommyds/tommyarrayblk.c \
-	src/tommyds/tommyarrayblkof.c \
-	src/tommyds/tommyhash.c \
-	src/tommyds/tommyhashdyn.c \
-	src/tommyds/tommylist.c \
-	src/portable.h \
-	src/snapraid.h \
-	src/util.h \
-	src/elem.h \
-	src/state.h \
-	src/parity.h \
-	src/handle.h \
-	src/murmur3.c \
-	src/murmur3test.c \
-	src/spooky2.c \
-	src/spooky2test.c \
-	src/fnmatch.h \
-	src/import.h \
-	src/mingw.h \
-	src/unix.h
+	raid/raid.h \
+	raid/helper.h \
+	raid/internal.h \
+	raid/cpu.h \
+	raid/gf.h \
+	raid/combo.h \
+	raid/memory.h \
+	raid/test.h \
+	tommyds/tommyarray.h \
+	tommyds/tommyarrayblk.h \
+	tommyds/tommyarrayblkof.h \
+	tommyds/tommychain.h \
+	tommyds/tommyhash.h \
+	tommyds/tommyhashdyn.h \
+	tommyds/tommylist.h \
+	tommyds/tommytypes.h \
+	tommyds/tommyarray.c \
+	tommyds/tommyarrayblk.c \
+	tommyds/tommyarrayblkof.c \
+	tommyds/tommyhash.c \
+	tommyds/tommyhashdyn.c \
+	tommyds/tommylist.c \
+	cmdline/portable.h \
+	cmdline/snapraid.h \
+	cmdline/util.h \
+	cmdline/elem.h \
+	cmdline/state.h \
+	cmdline/parity.h \
+	cmdline/handle.h \
+	cmdline/murmur3.c \
+	cmdline/murmur3test.c \
+	cmdline/spooky2.c \
+	cmdline/spooky2test.c \
+	cmdline/fnmatch.h \
+	cmdline/import.h \
+	cmdline/mingw.h \
+	cmdline/unix.h
 
 mktest_SOURCES = \
-	src/mktest.c \
-	src/mingw.c
+	cmdline/mktest.c \
+	cmdline/mingw.c
 
 EXTRA_DIST = \
 	autogen.sh \
@@ -94,13 +94,13 @@ EXTRA_DIST = \
 	snapraid.conf.example \
 	configure.windows-x86 configure.windows-x64 snapraid.conf.example.windows \
 	acinclude.m4 \
-	src/tommyds/LICENSE \
-	src/raid/COPYING \
-	src/raid/test/Makefile \
-	src/raid/test/fulltest.c \
-	src/raid/test/selftest.c \
-	src/raid/test/speedtest.c \
-	src/raid/test/invtest.c
+	tommyds/LICENSE \
+	raid/COPYING \
+	raid/test/Makefile \
+	raid/test/fulltest.c \
+	raid/test/selftest.c \
+	raid/test/speedtest.c \
+	raid/test/invtest.c
 
 man_MANS = snapraid.1
 
@@ -108,9 +108,9 @@ clean-local:
 	rm -f valgrind.log callgrind.log cachegrind.log
 	rm -rf bench
 	rm -f test*.log output.log
-	rm -f src/*.gcda src/*.gcno src/*.gcov
-	rm -f src/raid/*.gcda src/raid/*.gcno src/raid/*.gcov
-	rm -f src/tommyds/*.gcda src/tommyds/*.gcno src/tommyds/*.gcov
+	rm -f cmdline/*.gcda cmdline/*.gcno cmdline/*.gcov
+	rm -f raid/*.gcda raid/*.gcno raid/*.gcov
+	rm -f tommyds/*.gcda tommyds/*.gcno tommyds/*.gcov
 	rm -rf cov
 	rm -f lcov.info
 	rm -f gmon.out
@@ -617,11 +617,11 @@ cachegrind:
 		tail cachegrind.log
 
 lcov_reset:
-	lcov --directory src -z
+	lcov --directory . -z
 	rm -f ./lcov.info
 
 lcov_capture:
-	lcov --directory src --capture -o lcov.info
+	lcov --directory . --capture -o lcov.info
 
 lcov_html:
 	rm -rf ./cov
diff --git a/src/check.c b/cmdline/check.c
similarity index 100%
rename from src/check.c
rename to cmdline/check.c
diff --git a/src/dry.c b/cmdline/dry.c
similarity index 100%
rename from src/dry.c
rename to cmdline/dry.c
diff --git a/src/dup.c b/cmdline/dup.c
similarity index 100%
rename from src/dup.c
rename to cmdline/dup.c
diff --git a/src/elem.c b/cmdline/elem.c
similarity index 100%
rename from src/elem.c
rename to cmdline/elem.c
diff --git a/src/elem.h b/cmdline/elem.h
similarity index 100%
rename from src/elem.h
rename to cmdline/elem.h
diff --git a/src/fnmatch.c b/cmdline/fnmatch.c
similarity index 100%
rename from src/fnmatch.c
rename to cmdline/fnmatch.c
diff --git a/src/fnmatch.h b/cmdline/fnmatch.h
similarity index 100%
rename from src/fnmatch.h
rename to cmdline/fnmatch.h
diff --git a/src/handle.c b/cmdline/handle.c
similarity index 100%
rename from src/handle.c
rename to cmdline/handle.c
diff --git a/src/handle.h b/cmdline/handle.h
similarity index 100%
rename from src/handle.h
rename to cmdline/handle.h
diff --git a/src/import.c b/cmdline/import.c
similarity index 100%
rename from src/import.c
rename to cmdline/import.c
diff --git a/src/import.h b/cmdline/import.h
similarity index 100%
rename from src/import.h
rename to cmdline/import.h
diff --git a/src/list.c b/cmdline/list.c
similarity index 100%
rename from src/list.c
rename to cmdline/list.c
diff --git a/src/mingw.c b/cmdline/mingw.c
similarity index 100%
rename from src/mingw.c
rename to cmdline/mingw.c
diff --git a/src/mingw.h b/cmdline/mingw.h
similarity index 100%
rename from src/mingw.h
rename to cmdline/mingw.h
diff --git a/src/mktest.c b/cmdline/mktest.c
similarity index 100%
rename from src/mktest.c
rename to cmdline/mktest.c
diff --git a/src/murmur3.c b/cmdline/murmur3.c
similarity index 100%
rename from src/murmur3.c
rename to cmdline/murmur3.c
diff --git a/src/murmur3test.c b/cmdline/murmur3test.c
similarity index 100%
rename from src/murmur3test.c
rename to cmdline/murmur3test.c
diff --git a/src/parity.c b/cmdline/parity.c
similarity index 100%
rename from src/parity.c
rename to cmdline/parity.c
diff --git a/src/parity.h b/cmdline/parity.h
similarity index 100%
rename from src/parity.h
rename to cmdline/parity.h
diff --git a/src/pool.c b/cmdline/pool.c
similarity index 100%
rename from src/pool.c
rename to cmdline/pool.c
diff --git a/src/portable.h b/cmdline/portable.h
similarity index 100%
rename from src/portable.h
rename to cmdline/portable.h
diff --git a/src/rehash.c b/cmdline/rehash.c
similarity index 100%
rename from src/rehash.c
rename to cmdline/rehash.c
diff --git a/src/scan.c b/cmdline/scan.c
similarity index 100%
rename from src/scan.c
rename to cmdline/scan.c
diff --git a/src/scrub.c b/cmdline/scrub.c
similarity index 100%
rename from src/scrub.c
rename to cmdline/scrub.c
diff --git a/src/selftest.c b/cmdline/selftest.c
similarity index 100%
rename from src/selftest.c
rename to cmdline/selftest.c
diff --git a/src/snapraid.c b/cmdline/snapraid.c
similarity index 100%
rename from src/snapraid.c
rename to cmdline/snapraid.c
diff --git a/src/snapraid.h b/cmdline/snapraid.h
similarity index 100%
rename from src/snapraid.h
rename to cmdline/snapraid.h
diff --git a/src/speed.c b/cmdline/speed.c
similarity index 100%
rename from src/speed.c
rename to cmdline/speed.c
diff --git a/src/spooky2.c b/cmdline/spooky2.c
similarity index 100%
rename from src/spooky2.c
rename to cmdline/spooky2.c
diff --git a/src/spooky2test.c b/cmdline/spooky2test.c
similarity index 100%
rename from src/spooky2test.c
rename to cmdline/spooky2test.c
diff --git a/src/state.c b/cmdline/state.c
similarity index 100%
rename from src/state.c
rename to cmdline/state.c
diff --git a/src/state.h b/cmdline/state.h
similarity index 100%
rename from src/state.h
rename to cmdline/state.h
diff --git a/src/status.c b/cmdline/status.c
similarity index 100%
rename from src/status.c
rename to cmdline/status.c
diff --git a/src/sync.c b/cmdline/sync.c
similarity index 100%
rename from src/sync.c
rename to cmdline/sync.c
diff --git a/src/unix.c b/cmdline/unix.c
similarity index 100%
rename from src/unix.c
rename to cmdline/unix.c
diff --git a/src/unix.h b/cmdline/unix.h
similarity index 100%
rename from src/unix.h
rename to cmdline/unix.h
diff --git a/src/util.c b/cmdline/util.c
similarity index 100%
rename from src/util.c
rename to cmdline/util.c
diff --git a/src/util.h b/cmdline/util.h
similarity index 100%
rename from src/util.h
rename to cmdline/util.h
diff --git a/configure.ac b/configure.ac
index a11aa8a4..2d9d5365 100644
--- a/configure.ac
+++ b/configure.ac
@@ -2,7 +2,7 @@ dnl Process this file with autoconf to produce a configure script.
 AC_PREREQ([2.65])
 AC_INIT([snapraid], [6.0], [], [], [http://snapraid.sourceforge.net])
 AM_INIT_AUTOMAKE([foreign no-dependencies subdir-objects])
-AC_CONFIG_SRCDIR([src/snapraid.c])
+AC_CONFIG_SRCDIR([cmdline/snapraid.c])
 AC_CONFIG_HEADER([config.h])
 AC_CANONICAL_HOST
 
@@ -170,6 +170,9 @@ AC_ARG_ENABLE([warning],
 	],
 	[])
 
+dnl Default include dir for libraries
+CFLAGS="$CFLAGS $(srcdir)"
+
 AC_ARG_VAR([TESTENV], [Test environment])
 AC_ARG_VAR([FAILENV], [Test environment for failing tests])
 AC_CONFIG_FILES([Makefile])
diff --git a/src/raid/COPYING b/raid/COPYING
similarity index 100%
rename from src/raid/COPYING
rename to raid/COPYING
diff --git a/src/raid/combo.h b/raid/combo.h
similarity index 100%
rename from src/raid/combo.h
rename to raid/combo.h
diff --git a/src/raid/cpu.h b/raid/cpu.h
similarity index 100%
rename from src/raid/cpu.h
rename to raid/cpu.h
diff --git a/src/raid/gf.h b/raid/gf.h
similarity index 100%
rename from src/raid/gf.h
rename to raid/gf.h
diff --git a/src/raid/helper.c b/raid/helper.c
similarity index 100%
rename from src/raid/helper.c
rename to raid/helper.c
diff --git a/src/raid/helper.h b/raid/helper.h
similarity index 100%
rename from src/raid/helper.h
rename to raid/helper.h
diff --git a/src/raid/int.c b/raid/int.c
similarity index 100%
rename from src/raid/int.c
rename to raid/int.c
diff --git a/src/raid/internal.h b/raid/internal.h
similarity index 100%
rename from src/raid/internal.h
rename to raid/internal.h
diff --git a/src/raid/intz.c b/raid/intz.c
similarity index 100%
rename from src/raid/intz.c
rename to raid/intz.c
diff --git a/src/raid/memory.c b/raid/memory.c
similarity index 100%
rename from src/raid/memory.c
rename to raid/memory.c
diff --git a/src/raid/memory.h b/raid/memory.h
similarity index 100%
rename from src/raid/memory.h
rename to raid/memory.h
diff --git a/src/raid/mktables.c b/raid/mktables.c
similarity index 100%
rename from src/raid/mktables.c
rename to raid/mktables.c
diff --git a/src/raid/module.c b/raid/module.c
similarity index 100%
rename from src/raid/module.c
rename to raid/module.c
diff --git a/src/raid/raid.c b/raid/raid.c
similarity index 100%
rename from src/raid/raid.c
rename to raid/raid.c
diff --git a/src/raid/raid.h b/raid/raid.h
similarity index 100%
rename from src/raid/raid.h
rename to raid/raid.h
diff --git a/src/raid/sort.c b/raid/sort.c
similarity index 100%
rename from src/raid/sort.c
rename to raid/sort.c
diff --git a/src/raid/tables.c b/raid/tables.c
similarity index 100%
rename from src/raid/tables.c
rename to raid/tables.c
diff --git a/src/raid/tag.c b/raid/tag.c
similarity index 100%
rename from src/raid/tag.c
rename to raid/tag.c
diff --git a/src/raid/test.c b/raid/test.c
similarity index 100%
rename from src/raid/test.c
rename to raid/test.c
diff --git a/src/raid/test.h b/raid/test.h
similarity index 100%
rename from src/raid/test.h
rename to raid/test.h
diff --git a/src/raid/test/Makefile b/raid/test/Makefile
similarity index 100%
rename from src/raid/test/Makefile
rename to raid/test/Makefile
diff --git a/src/raid/test/fulltest.c b/raid/test/fulltest.c
similarity index 100%
rename from src/raid/test/fulltest.c
rename to raid/test/fulltest.c
diff --git a/src/raid/test/invtest.c b/raid/test/invtest.c
similarity index 100%
rename from src/raid/test/invtest.c
rename to raid/test/invtest.c
diff --git a/src/raid/test/selftest.c b/raid/test/selftest.c
similarity index 100%
rename from src/raid/test/selftest.c
rename to raid/test/selftest.c
diff --git a/src/raid/test/speedtest.c b/raid/test/speedtest.c
similarity index 100%
rename from src/raid/test/speedtest.c
rename to raid/test/speedtest.c
diff --git a/src/raid/x86.c b/raid/x86.c
similarity index 100%
rename from src/raid/x86.c
rename to raid/x86.c
diff --git a/src/raid/x86z.c b/raid/x86z.c
similarity index 100%
rename from src/raid/x86z.c
rename to raid/x86z.c
diff --git a/src/tommyds/LICENSE b/tommyds/LICENSE
similarity index 100%
rename from src/tommyds/LICENSE
rename to tommyds/LICENSE
diff --git a/src/tommyds/tommy.c b/tommyds/tommy.c
similarity index 92%
rename from src/tommyds/tommy.c
rename to tommyds/tommy.c
index b826e56f..4b2cce3b 100644
--- a/src/tommyds/tommy.c
+++ b/tommyds/tommy.c
@@ -15,8 +15,8 @@
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include "../portable.h"
-#include "../util.h" /* for safe_malloc */
+#include "cmdline/portable.h"
+#include "cmdline/util.h" /* for safe_malloc */
 
 /* redefine the malloc for tommy use */
 #define tommy_malloc malloc_nofail
diff --git a/src/tommyds/tommyarray.c b/tommyds/tommyarray.c
similarity index 100%
rename from src/tommyds/tommyarray.c
rename to tommyds/tommyarray.c
diff --git a/src/tommyds/tommyarray.h b/tommyds/tommyarray.h
similarity index 100%
rename from src/tommyds/tommyarray.h
rename to tommyds/tommyarray.h
diff --git a/src/tommyds/tommyarrayblk.c b/tommyds/tommyarrayblk.c
similarity index 100%
rename from src/tommyds/tommyarrayblk.c
rename to tommyds/tommyarrayblk.c
diff --git a/src/tommyds/tommyarrayblk.h b/tommyds/tommyarrayblk.h
similarity index 100%
rename from src/tommyds/tommyarrayblk.h
rename to tommyds/tommyarrayblk.h
diff --git a/src/tommyds/tommyarrayblkof.c b/tommyds/tommyarrayblkof.c
similarity index 100%
rename from src/tommyds/tommyarrayblkof.c
rename to tommyds/tommyarrayblkof.c
diff --git a/src/tommyds/tommyarrayblkof.h b/tommyds/tommyarrayblkof.h
similarity index 100%
rename from src/tommyds/tommyarrayblkof.h
rename to tommyds/tommyarrayblkof.h
diff --git a/src/tommyds/tommychain.h b/tommyds/tommychain.h
similarity index 100%
rename from src/tommyds/tommychain.h
rename to tommyds/tommychain.h
diff --git a/src/tommyds/tommyhash.c b/tommyds/tommyhash.c
similarity index 100%
rename from src/tommyds/tommyhash.c
rename to tommyds/tommyhash.c
diff --git a/src/tommyds/tommyhash.h b/tommyds/tommyhash.h
similarity index 100%
rename from src/tommyds/tommyhash.h
rename to tommyds/tommyhash.h
diff --git a/src/tommyds/tommyhashdyn.c b/tommyds/tommyhashdyn.c
similarity index 100%
rename from src/tommyds/tommyhashdyn.c
rename to tommyds/tommyhashdyn.c
diff --git a/src/tommyds/tommyhashdyn.h b/tommyds/tommyhashdyn.h
similarity index 100%
rename from src/tommyds/tommyhashdyn.h
rename to tommyds/tommyhashdyn.h
diff --git a/src/tommyds/tommylist.c b/tommyds/tommylist.c
similarity index 100%
rename from src/tommyds/tommylist.c
rename to tommyds/tommylist.c
diff --git a/src/tommyds/tommylist.h b/tommyds/tommylist.h
similarity index 100%
rename from src/tommyds/tommylist.h
rename to tommyds/tommylist.h
diff --git a/src/tommyds/tommytypes.h b/tommyds/tommytypes.h
similarity index 100%
rename from src/tommyds/tommytypes.h
rename to tommyds/tommytypes.h