Taken from gentoo portage.

# posted to bug #251796 by <andrex@mail.ee> from Debian patches
diff -u -r pdftk-1.41.orig/java_libs/com/lowagie/bc/asn1/Makefile pdftk-1.41/java_libs/com/lowagie/bc/asn1/Makefile
--- pdftk-1.41.orig/java_libs/com/lowagie/bc/asn1/Makefile	2008-12-22 23:43:29.000000000 +0200
+++ pdftk-1.41/java_libs/com/lowagie/bc/asn1/Makefile	2008-12-23 00:04:52.000000000 +0200
@@ -25,8 +25,7 @@
 # the "$*" automatic variable, here
 #
 %.h : %.class
-	$(GCJH) --classpath="." $*;
-	$(RM) $<
+	$(GCJH) --classpath="$(java_libs_root):." $*;
 
 ##
 # targets
diff -u -r pdftk-1.41.orig/java_libs/com/lowagie/text/Makefile pdftk-1.41/java_libs/com/lowagie/text/Makefile
--- pdftk-1.41.orig/java_libs/com/lowagie/text/Makefile	2008-12-22 23:43:29.000000000 +0200
+++ pdftk-1.41/java_libs/com/lowagie/text/Makefile	2008-12-22 23:58:52.000000000 +0200
@@ -25,13 +25,12 @@
 # the "$*" automatic variable, here
 #
 %.h : %.class
-	$(GCJH) --classpath="." $*;
-	$(RM) $<
+	$(GCJH) --classpath="$(java_libs_root):." $*;
 
 ##
 # targets
 
-all : $(library) $(headers)
+all : $(library) $(headers) $(classes)
 
 $(library) : $(objects)
 	$(AR) $(ARFLAGS) $(library) $(objects);
diff -u -r pdftk-1.41.orig/java_libs/com/lowagie/text/markup/Makefile pdftk-1.41/java_libs/com/lowagie/text/markup/Makefile
--- pdftk-1.41.orig/java_libs/com/lowagie/text/markup/Makefile	2008-12-22 23:43:29.000000000 +0200
+++ pdftk-1.41/java_libs/com/lowagie/text/markup/Makefile	2008-12-23 00:04:28.000000000 +0200
@@ -25,8 +25,7 @@
 # the "$*" automatic variable, here
 #
 %.h : %.class
-	$(GCJH) --classpath="." $*;
-	$(RM) $<
+	$(GCJH) --classpath="$(java_libs_root):." $*;
 
 ##
 # targets
diff -u -r pdftk-1.41.orig/java_libs/com/lowagie/text/pdf/codec/Makefile pdftk-1.41/java_libs/com/lowagie/text/pdf/codec/Makefile
--- pdftk-1.41.orig/java_libs/com/lowagie/text/pdf/codec/Makefile	2008-12-22 23:43:29.000000000 +0200
+++ pdftk-1.41/java_libs/com/lowagie/text/pdf/codec/Makefile	2008-12-23 00:04:11.000000000 +0200
@@ -25,8 +25,7 @@
 # the "$*" automatic variable, here
 #
 %.h : %.class
-	$(GCJH) --classpath="." $*;
-	$(RM) $<
+	$(GCJH) --classpath="$(java_libs_root):." $*;
 
 ##
 # targets
diff -u -r pdftk-1.41.orig/java_libs/com/lowagie/text/pdf/codec/postscript/Makefile pdftk-1.41/java_libs/com/lowagie/text/pdf/codec/postscript/Makefile
--- pdftk-1.41.orig/java_libs/com/lowagie/text/pdf/codec/postscript/Makefile	2008-12-22 23:43:29.000000000 +0200
+++ pdftk-1.41/java_libs/com/lowagie/text/pdf/codec/postscript/Makefile	2008-12-23 00:03:05.000000000 +0200
@@ -25,8 +25,7 @@
 # the "$*" automatic variable, here
 #
 %.h : %.class
-	$(GCJH) --classpath="." $*;
-	$(RM) $<
+	$(GCJH) --classpath="$(java_libs_root):." $*;
 
 ##
 # targets
diff -u -r pdftk-1.41.orig/java_libs/com/lowagie/text/pdf/codec/wmf/Makefile pdftk-1.41/java_libs/com/lowagie/text/pdf/codec/wmf/Makefile
--- pdftk-1.41.orig/java_libs/com/lowagie/text/pdf/codec/wmf/Makefile	2008-12-22 23:43:29.000000000 +0200
+++ pdftk-1.41/java_libs/com/lowagie/text/pdf/codec/wmf/Makefile	2008-12-23 00:03:29.000000000 +0200
@@ -25,8 +25,7 @@
 # the "$*" automatic variable, here
 #
 %.h : %.class
-	$(GCJH) --classpath="." $*;
-	$(RM) $<
+	$(GCJH) --classpath="$(java_libs_root):." $*;
 
 ##
 # targets
diff -u -r pdftk-1.41.orig/java_libs/com/lowagie/text/pdf/fonts/Makefile pdftk-1.41/java_libs/com/lowagie/text/pdf/fonts/Makefile
--- pdftk-1.41.orig/java_libs/com/lowagie/text/pdf/fonts/Makefile	2008-12-22 23:43:29.000000000 +0200
+++ pdftk-1.41/java_libs/com/lowagie/text/pdf/fonts/Makefile	2008-12-23 00:01:33.000000000 +0200
@@ -34,8 +34,7 @@
 # the "$*" automatic variable, here
 #
 %.h : %.class
-	$(GCJH) --classpath="." $*;
-	$(RM) $<
+	$(GCJH) --classpath="$(java_libs_root):." $*;
 
 ##
 # targets
diff -u -r pdftk-1.41.orig/java_libs/com/lowagie/text/pdf/Makefile pdftk-1.41/java_libs/com/lowagie/text/pdf/Makefile
--- pdftk-1.41.orig/java_libs/com/lowagie/text/pdf/Makefile	2008-12-22 23:43:29.000000000 +0200
+++ pdftk-1.41/java_libs/com/lowagie/text/pdf/Makefile	2008-12-23 00:00:25.000000000 +0200
@@ -25,8 +25,7 @@
 # the "$*" automatic variable, here
 #
 %.h : %.class
-	$(GCJH) --classpath="." $*;
-	$(RM) $<
+	$(GCJH) --classpath="$(java_libs_root):." $*;
 
 ##
 # targets
diff -u -r pdftk-1.41.orig/java_libs/com/lowagie/text/pdf/PdfEncryption.java pdftk-1.41/java_libs/com/lowagie/text/pdf/PdfEncryption.java
--- pdftk-1.41.orig/java_libs/com/lowagie/text/pdf/PdfEncryption.java	2008-12-22 23:43:29.000000000 +0200
+++ pdftk-1.41/java_libs/com/lowagie/text/pdf/PdfEncryption.java	2008-12-22 23:46:21.000000000 +0200
@@ -50,7 +50,7 @@
 
 package com.lowagie.text.pdf;
 
-import java_local.security.MessageDigest; // ssteward
+import java.security.MessageDigest;
 import com.lowagie.text.ExceptionConverter;
 
 /**
diff -u -r pdftk-1.41.orig/java_libs/com/lowagie/text/xml/xmp/Makefile pdftk-1.41/java_libs/com/lowagie/text/xml/xmp/Makefile
--- pdftk-1.41.orig/java_libs/com/lowagie/text/xml/xmp/Makefile	2008-12-22 23:43:29.000000000 +0200
+++ pdftk-1.41/java_libs/com/lowagie/text/xml/xmp/Makefile	2008-12-22 23:59:42.000000000 +0200
@@ -25,8 +25,7 @@
 # the "$*" automatic variable, here
 #
 %.h : %.class
-	$(GCJH) --classpath="." $*;
-	$(RM) $<
+	$(GCJH) --classpath="$(java_libs_root):." $*;
 
 ##
 # targets
diff -u -r pdftk-1.41.orig/java_libs/Makefile pdftk-1.41/java_libs/Makefile
--- pdftk-1.41.orig/java_libs/Makefile	2008-12-22 23:43:29.000000000 +0200
+++ pdftk-1.41/java_libs/Makefile	2008-12-22 23:47:10.000000000 +0200
@@ -13,13 +13,7 @@
 # append gcj flags
 export GCJFLAGS+= --encoding=UTF-8 --classpath="$(java_libs_root)"
 
-all : libgcj_local itext
-
-libgcj_local :
-	$(MAKE) -C "$(java_libs_root)/gnu_local/java/security";
-	$(MAKE) -C "$(java_libs_root)/gnu_local/java/security/provider";
-	$(MAKE) -C "$(java_libs_root)/gnu/gcj/convert";
-	$(MAKE) -C "$(java_libs_root)/java_local/security";
+all : itext
 
 itext :
 	$(MAKE) -C "$(java_libs_root)/com/lowagie/text";
@@ -35,13 +29,7 @@
 	$(MAKE) -C "$(java_libs_root)/com/lowagie/bc/asn1";
 	$(MAKE) -C "$(java_libs_root)/com/lowagie/text/pdf/codec/postscript";
 
-clean : libgcj_local_clean itext_clean
-
-libgcj_local_clean :
-	$(MAKE) -iC "$(java_libs_root)/gnu_local/java/security" clean;
-	$(MAKE) -iC "$(java_libs_root)/gnu_local/java/security/provider" clean;
-	$(MAKE) -iC "$(java_libs_root)/gnu/gcj/convert" clean;
-	$(MAKE) -iC "$(java_libs_root)/java_local/security" clean;
+clean : itext_clean
 
 itext_clean :
 	$(MAKE) -iC "$(java_libs_root)/com/lowagie/text" clean;
diff -u -r pdftk-1.41.orig/pdftk/Makefile.Base pdftk-1.41/pdftk/Makefile.Base
--- pdftk-1.41.orig/pdftk/Makefile.Base	2008-12-22 23:43:29.000000000 +0200
+++ pdftk-1.41/pdftk/Makefile.Base	2008-12-22 23:44:33.000000000 +0200
@@ -31,18 +31,6 @@
 afms= $(wildcard $(java_libs_root)/com/lowagie/text/pdf/fonts/*.afm)
 afm_objects= $(patsubst %.afm, %.o, $(afms))
 
-# older versions of libgcj might not have the MD5 algorithm,
-# so I added it here; these *_local java files were grabbed from
-# libgcj CVS on March 7, 2004; diffed September 5, 2006 w/ gcc 4.1.1
-#
-# gnu/gcj/convert/Input_UnicodeBig.java was grabbed March 26, 2004; diffed September 5, 2006 w/ gcc 4.1.1
-#
-libgcj_local_libs = \
-$(java_libs_root)/java_local/security/security.a \
-$(java_libs_root)/gnu_local/java/security/provider/provider.a \
-$(java_libs_root)/gnu_local/java/security/security.a \
-$(java_libs_root)/gnu/gcj/convert/convert.a
-
 # this must already be set according to your platform Makefile;
 # we're just appending to it, here
 #
diff -u -r pdftk-1.41.orig/pdftk/Makefile.Generic pdftk-1.41/pdftk/Makefile.Generic
--- pdftk-1.41.orig/pdftk/Makefile.Generic	2008-12-22 23:43:29.000000000 +0200
+++ pdftk-1.41/pdftk/Makefile.Generic	2008-12-23 00:06:24.000000000 +0200
@@ -28,7 +28,7 @@
 
 # itext compiler flags
 # -O3 might cause pdftk to segfault on cat operation (gcc 3.4.4)
-export GCJFLAGS= -O2
+export GCJFLAGS= -O2 -w
 
 #
 export ARFLAGS= rs
