diff --git a/clean.sh b/clean.sh
index 04b0d77..9d6c824 100755
--- a/clean.sh
+++ b/clean.sh
@@ -14,5 +14,6 @@ find . | perl -ne 'print if (/\/storefile.txt$/)' | xargs rm -f
 find . | perl -ne 'print if (/\/logfile.txt$/)' | xargs rm -f
 find . | perl -ne 'print if (/\/blob._file.txt$/)' | xargs rm -f
 rm -f test/gmon.out test/lladd/gmon.out
-rm -f m4/ltsugar.m4 m4/libtool.m4 m4/ltversion.m4 m4/lt~obsolete.m4 m4/ltoptions.m4
 rm -f configure.in
+rm -f config.guess config.h config.log config.status config.sub install-sh ltmain.sh mkinstalldirs py-compile
+rm -f m4/ltsugar.m4 m4/libtool.m4 m4/ltversion.m4 m4/lt~obsolete.m4 m4/ltoptions.m4 missing stamp-h1
diff --git a/cvs-branch-info b/cvs-branch-info
deleted file mode 100644
index 6693040..0000000
--- a/cvs-branch-info
+++ /dev/null
@@ -1,6 +0,0 @@
-5-1-05 RCS did this:
-
-Created branch for blast stuff:
-
-cvs tag -b blast
-cvs checkout -r blast lladd
diff --git a/mkinstalldirs b/mkinstalldirs
deleted file mode 100755
index 6b3b5fc..0000000
--- a/mkinstalldirs
+++ /dev/null
@@ -1,40 +0,0 @@
-#! /bin/sh
-# mkinstalldirs --- make directory hierarchy
-# Author: Noah Friedman <friedman@prep.ai.mit.edu>
-# Created: 1993-05-16
-# Public domain
-
-# $Id$
-
-errstatus=0
-
-for file
-do
-   set fnord `echo ":$file" | sed -ne 's/^:\//#/;s/^://;s/\// /g;s/^#/\//;p'`
-   shift
-
-   pathcomp=
-   for d
-   do
-     pathcomp="$pathcomp$d"
-     case "$pathcomp" in
-       -* ) pathcomp=./$pathcomp ;;
-     esac
-
-     if test ! -d "$pathcomp"; then
-        echo "mkdir $pathcomp"
-
-        mkdir "$pathcomp" || lasterr=$?
-
-        if test ! -d "$pathcomp"; then
-  	  errstatus=$lasterr
-        fi
-     fi
-
-     pathcomp="$pathcomp/"
-   done
-done
-
-exit $errstatus
-
-# mkinstalldirs ends here
diff --git a/reconf b/reconf
index 6e98879..db4734c 100755
--- a/reconf
+++ b/reconf
@@ -121,7 +121,19 @@ Proceeding with system's default automake.  Expect trouble.
    $ENV{AUTOMAKE} = "$automake_base-$version";
 }
 
+my $rmNEWS = 1;
+my $rmChangeLog = 1;
+if(-f "NEWS") { $rmNEWS = 0; } else { system("touch NEWS"); }
+if(-f "ChangeLog") { $rmChangeLog = 0; }  else { system("touch ChangeLog"); }
+
+
+
 system("rm configure.in");
 system("ln -s configure.in.automake configure.in");
 
 system ("autoreconf -i", @ARGV);
+
+if($rmNEWS) { system("rm NEWS"); }
+if($rmChangeLog) { system("rm ChangeLog"); }
+
+
diff --git a/stamp-h.in b/stamp-h.in
deleted file mode 100644
index 9788f70..0000000
--- a/stamp-h.in
+++ /dev/null
@@ -1 +0,0 @@
-timestamp