diff --git a/.gitignore b/.gitignore
new file mode 100644
index 00000000..e7a27eac
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,76 @@
+# Generic auto-generated build files
+*~
+*.a
+*.la
+*.lai
+*.lo
+*.Plo
+*.Po
+*.o
+*.so
+*.so.[0-9][0-9]*
+*.so.[0-9][0-9]*.[0-9][0-9]*.[0-9][0-9]*
+*.Tpo
+.deps
+.libs
+INSTALL
+Makefile
+Makefile.in
+stamp-h1
+
+# Specific auto-generated build files
+/ABOUT-NLS
+/aclocal.m4
+/ar-lib
+/autom4te.cache/
+/config.guess
+/config.h.in
+/config.log
+/config.rpath
+/config.status
+/config.sub
+/configure
+/depcomp
+/install-sh
+/libtool
+/ltmain.sh
+/missing
+/ylwrap
+/m4/codeset.m4
+/m4/fcntl-o.m4
+/m4/gettext.m4
+/m4/glibc2.m4
+/m4/glibc21.m4
+/m4/iconv.m4
+/m4/intdiv0.m4
+/m4/intl.m4
+/m4/intldir.m4
+/m4/intlmacosx.m4
+/m4/intmax.m4
+/m4/inttypes-pri.m4
+/m4/inttypes_h.m4
+/m4/lcmessage.m4
+/m4/lib-ld.m4
+/m4/lib-link.m4
+/m4/lib-prefix.m4
+/m4/libtool.m4
+/m4/lock.m4
+/m4/longlong.m4
+/m4/ltoptions.m4
+/m4/ltsugar.m4
+/m4/ltversion.m4
+/m4/lt~obsolete.m4
+/m4/progtest.m4
+/m4/printf-posix.m4
+/m4/size_max.m4
+/m4/stdint_h.m4
+/m4/threadlib.m4
+/m4/uintmax_t.m4
+/m4/visibility.m4
+/m4/wchar_t.m4
+/m4/wint_t.m4
+/m4/xsize.m4
+
+# Project specific files
+/yara
+/yarac
diff --git a/bootstrap.sh b/bootstrap.sh
index e97442c0..d716e8aa 100755
--- a/bootstrap.sh
+++ b/bootstrap.sh
@@ -34,7 +34,7 @@ autogen() {
 
   echo "aclocal..."
   if test x$ACLOCAL = x; then
-    ACLOCAL=`locate_binary aclocal-1.11 aclocal-1.10 aclocal-1.9 aclocal19 aclocal-1.7 aclocal17 aclocal-1.5 aclocal15 aclocal`
+    ACLOCAL=`locate_binary aclocal aclocal-1.11 aclocal-1.10 aclocal-1.9 aclocal19 aclocal-1.7 aclocal17 aclocal-1.5 aclocal15`
     if test x$ACLOCAL = x; then
       die "Did not find a supported aclocal"
     fi
@@ -47,7 +47,7 @@ autogen() {
 
   echo "automake..."
   if test x$AUTOMAKE = x; then
-    AUTOMAKE=`locate_binary automake-1.14 automake-1.3 automake-1.12 automake-1.11 automake-1.10 automake-1.9 automake-1.7 automake`
+    AUTOMAKE=`locate_binary automake automake-1.14 automake-1.3 automake-1.12 automake-1.11 automake-1.10 automake-1.9 automake-1.7`
     if test x$AUTOMAKE = x; then
       die "Did not find a supported automake"
     fi
@@ -62,7 +62,3 @@ autogen() {
 
 echo "== bootstraping yara"
 autogen
-echo "== bootstraping libyara"
-cd libyara
-autogen
-cd ..
\ No newline at end of file
diff --git a/config.h b/config.h
index f5b04843..8c492867 100644
--- a/config.h
+++ b/config.h
@@ -1,12 +1,18 @@
 /* config.h.  Generated from config.h.in by configure.  */
 /* config.h.in.  Generated from configure.ac by autoheader.  */
 
+/* enable dmalloc */
+/* #undef DMALLOC */
+
 /* Define to 1 if you have the <dlfcn.h> header file. */
 #define HAVE_DLFCN_H 1
 
 /* Define to 1 if you have the <inttypes.h> header file. */
 #define HAVE_INTTYPES_H 1
 
+/* Define to 1 if you have the `dmalloc' library (-ldmalloc). */
+/* #undef HAVE_LIBDMALLOC */
+
 /* Define to 1 if you have the `pthread' library (-lpthread). */
 #define HAVE_LIBPTHREAD 1
 
@@ -53,6 +59,9 @@
 /* Define to the one symbol short name of this package. */
 #define PACKAGE_TARNAME "yara"
 
+/* Define to the home page for this package. */
+#define PACKAGE_URL ""
+
 /* Define to the version of this package. */
 #define PACKAGE_VERSION "2.0"
 
@@ -61,3 +70,7 @@
 
 /* Version number of package */
 #define VERSION "2.0"
+
+/* Define to 1 if `lex' declares `yytext' as a `char *' by default, not a
+   `char[]'. */
+/* #undef YYTEXT_POINTER */
diff --git a/configure.ac b/configure.ac
index d3fc9b6a..d2635b62 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,25 +1,35 @@
 AC_INIT([yara], [2.0], [vmalvarez@virustotal.com])
 
+AC_CONFIG_SRCDIR([yara.c])
+
+AM_INIT_AUTOMAKE([-Wall -Werror foreign])
+
+AC_CONFIG_MACRO_DIR([m4])
+
 ${CFLAGS=""}
 
 # automake 1.12 seems to require AM_PROG_AR, but automake 1.11 doesn't
 # recognize it
-
 m4_ifdef([AM_PROG_AR], [AM_PROG_AR])
 
-LT_INIT
-AM_INIT_AUTOMAKE([-Wall -Werror foreign])
 AC_PROG_CC
+AM_PROG_LEX
+AC_PROG_YACC
+
+LT_INIT
 AC_PROG_LIBTOOL
-AC_CONFIG_MACRO_DIR([m4])
-AC_CONFIG_HEADERS([config.h])
-AC_CONFIG_FILES([Makefile])
-AC_CONFIG_SUBDIRS([libyara])
-AC_CHECK_LIB(pthread, pthread_create)
+
 AC_ARG_ENABLE([dmalloc],
   [AS_HELP_STRING([--enable-dmalloc], [enable dmalloc to debug heap-related issues])],
   [if test x$enableval = xyes; then
     AC_CHECK_LIB(dmalloc, dmalloc_malloc,, AC_MSG_ERROR(please install dmalloc library))
     AC_DEFINE([DMALLOC], [], [enable dmalloc])
   fi])
+
+AC_CHECK_LIB(pthread, pthread_create)
+
+AC_CONFIG_FILES([Makefile])
+AC_CONFIG_FILES([libyara/Makefile])
+AC_CONFIG_HEADERS([config.h])
+
 AC_OUTPUT
diff --git a/libyara/configure.ac b/libyara/configure.ac
deleted file mode 100644
index a08b022e..00000000
--- a/libyara/configure.ac
+++ /dev/null
@@ -1,25 +0,0 @@
-AC_INIT([libyara], [2.0], [vmalvarez@virustotal.com])
-
-${CFLAGS=""}
-
-# automake 1.12 seems to require AM_PROG_AR, but automake 1.11 doesn't
-# recognize it
-
-m4_ifdef([AM_PROG_AR], [AM_PROG_AR])
-
-LT_INIT
-AM_INIT_AUTOMAKE([-Wall -Werror foreign])
-AC_PROG_CC
-AC_PROG_YACC
-AM_PROG_LEX
-AC_PROG_LIBTOOL
-AC_CONFIG_MACRO_DIR([m4])
-AC_CONFIG_HEADERS([config.h])
-AC_ARG_ENABLE([dmalloc],
-  [AS_HELP_STRING([--enable-dmalloc], [enable dmalloc to debug heap-related issues])],
-  [if test x$enableval = xyes; then
-    AC_CHECK_LIB(dmalloc, dmalloc_malloc,, AC_MSG_ERROR(please install dmalloc library))
-    AC_DEFINE([DMALLOC], [], [enable dmalloc])
-  fi])
-AC_CONFIG_FILES([Makefile])
-AC_OUTPUT