diff --git a/bootstrap b/bootstrap
index 3cb1458..278c3e9 100755
--- a/bootstrap
+++ b/bootstrap
@@ -1,6 +1,9 @@
 #! /bin/sh
 
-aclocal \
-&& automake --gnu --add-missing \
-&& autoconf
+set -x
+aclocal -I config
+libtoolize --force --copy
+autoheader
+automake --add-missing --copy --foreign
+autoconf
 
diff --git a/configure.in b/configure.in
index 97d63ab..adee5ba 100644
--- a/configure.in
+++ b/configure.in
@@ -1,29 +1,36 @@
-AC_INIT(main.c)
+AC_INIT(src/main.c)
 AM_INIT_AUTOMAKE(Scyther, 0.2, ccremers@win.tue.nl)
-AC_CONFIG_SRCDIR([src/modelchecker.c])
-            
+AC_CONFIG_AUX_DIR(config)
+AM_CONFIG_HEADER(config.h)
+AC_CONFIG_SRCDIR(src)
+
+for top_builddir in . .. ../.. $ac_auxdir $ac_auxdir/..; do
+  test -f $top_builddir/configure && break
+done
+AC_PROG_LIBTOOL
+
 dnl find and test the C compiler
 AC_PROG_CC
 AC_LANG_C
-AC_PROG_INSTALL
+AC_PROG_INSTALL=$ac_aux_dir
         
 AC_PROG_MAKE_SET
 
 # Checks for header files.
 AC_HEADER_STDC
 AC_CHECK_HEADERS([limits.h malloc.h stddef.h stdlib.h strings.h unistd.h])
-
 # Checks for library functions.
 AC_FUNC_MALLOC
 AC_FUNC_REALLOC
                
 AC_CHECK_LIB(argtable2, arg_parse,,AC_MSG_ERROR(Scyther requires the argtable2 package (LGPL). Get it from http://argtable.sourceforge.net/))
 AC_PROG_YACC
-AM_PROG_LEX
+AC_PROG_LEX
+#AC_DECL_YYTEXT
                   
 VERSION="0.0.1"
-AC_SUBST(VERSION)
-AC_CONFIG_AUX_DIR(config)
+AC_SUBST(ac_aux_dir)
+SUBDIRS = src 
 
 dnl read Makefile.in and write Makefile
-AC_OUTPUT(Makefile)
+AC_OUTPUT(Makefile src/Makefile)
diff --git a/src/Makefile b/src/Makefile
deleted file mode 100644
index 28feff5..0000000
--- a/src/Makefile
+++ /dev/null
@@ -1,87 +0,0 @@
-#
-#	Scyther Makefile
-#
-
-#
-#	DEBUG or optimization settings: uncomment a single line:
-#
-CFLAGS = -g3 -D DEBUG		# default usage, for e.g. with valgrind
-#CFLAGS = -g3 -D DEBUG -pg	# for code profiling with gprof
-#CFLAGS = -O3 -static -finline-functions -fomit-frame-pointer
-
-#
-#	Compiler and linkage
-#
-CC = gcc
-# Note that these paths must include the path to the argtable library.
-CPPFLAGS = -I/scratch/ccremers/include -I/usr/local/include -Wall
-LDFLAGS = -L/scratch/ccremers/lib -L/usr/local/lib
-LOADLIBS = -lfl
-LDLIBS = -largtable2
-OPTIONS = ${CPPFLAGS} ${CFLAGS} ${LDFLAGS}
-
-#
-#	Module set for the modelchecker
-#
-MODULES=memory.o terms.o termlists.o symbols.o knowledge.o runs.o modelchecker.o \
-report.o debug.o  mgu.o substitutions.o \
-match_basic.o \
-match_clp.o constraints.o \
-output.o latex.o \
-varbuf.o tracebuf.o attackminimize.o \
-tac.o parser.o compiler.o 
-
-#
-#	Dependencies
-#
-MODELCHECKER = ${MODULES} main.o
-
-all:		scyther tags
-
-${Target}.o:	${Target}.c
-		$(CC) $(OPTIONS) ${Target}.c -c
-
-scanner.c:	scanner.l
-		flex scanner.l
-		cp lex.yy.c scanner.c
-
-tok.h:		parser.c
-
-parser.c:	parser.y
-		bison -d -v parser.y
-		cp parser.tab.c parser.c
-		cmp -s parser.tab.h tok.h || cp parser.tab.h tok.h
-		cmp -s parser.tab.h parser.h || cp parser.tab.h parser.h
-
-tags:		*.c *.h
-		ctags *.c *.h
-
-modules:	$(MODULES)
-
-scyther:	scanner.o $(MODELCHECKER)
-		$(CC) $(OPTIONS) $(MODELCHECKER) -o scyther $(LOADLIBS) $(LDLIBS)
-
-ptestmain.o scanner.o	: tok.h
-
-#
-#	Cleanup
-#
-clean:
-		rm -f *.o
-		rm -f scyther
-		rm -f scanner.c
-		rm -f parser.c
-		rm -f tok.h
-#
-#	Clean and rebuild: 'make new'
-#
-new:
-		make clean
-		make all
-
-#
-#	Make doxygen reference manuals. (in ../refman)
-#
-refman:		doxyconfig
-		doxygen doxyconfig
-
diff --git a/Makefile.am b/src/Makefile.am
similarity index 90%
rename from Makefile.am
rename to src/Makefile.am
index d2636d1..4493628 100644
--- a/Makefile.am
+++ b/src/Makefile.am
@@ -4,14 +4,13 @@ AM_CFLAGS = @CFLAGS@
 
 bin_PROGRAMS = scyther
 scyther_SOURCES = main.c \
+		 scanner.l parser.y \
 		 memory.c terms.c termlists.c symbols.c \
 		 knowledge.c runs.c modelchecker.c \
 		 report.c debug.c mgu.c substitutions.c \
 		 match_basic.c match_clp.c constraints.c \
 		 output.c latex.c varbuf.c tracebuf.c \
 		 attackminimize.c tac.c \
-		 compiler.c \
-		 scanner.l parser.y
+		 compiler.c 
 scyther_LDADD = @LEXLIB@
 
-
diff --git a/src/latex.c b/src/latex.c
index 9dde12e..a0b9e37 100644
--- a/src/latex.c
+++ b/src/latex.c
@@ -912,7 +912,7 @@ attackDisplayLatex (System sys)
 
 	  /* put out computed widths */
 	  
-	  printf ("\\setlength{\\envinstdist}{0.5\\maxmscall}\n");
+	  printf ("\\setlength{\\envinstdist}{0.7\\maxmscall}\n");
 	  printf ("\\setlength{\\instdist}{\\maxmscall}\n");
 	  printf ("\\setlength{\\actionwidth}{\\maxmscaction}\n");
 	  printf ("\\setlength{\\instwidth}{\\maxmscinst}\n");
diff --git a/src/main.c b/src/main.c
index d514176..ff9bac7 100644
--- a/src/main.c
+++ b/src/main.c
@@ -36,7 +36,7 @@
 #include "symbols.h"
 #include "pheading.h"
 #include "symbols.h"
-#include "parser.h"
+#include "parser.tab.h"
 #include "tac.h"
 #include "compiler.h"
 #include "latex.h"
diff --git a/src/parser.y b/src/parser.y
index 75b0b4b..52d3a91 100644
--- a/src/parser.y
+++ b/src/parser.y
@@ -1,6 +1,6 @@
 %{
 #include "pheading.h"
-#include "scanner.c"
+/* #include "lex.yy.c" */
 #include "tac.h"
 
 struct tacnode*	spdltac;