Based on https://anonscm.debian.org/viewvc/pkg-java/trunk/libxerces2-java/debian/patches/03_bootclasspath.patch?revision=14509, adopted for guix

--- xerces-2_11_0/build.xml.orig	2010-11-26 21:42:11.000000000 +0100
+++ xerces-2_11_0/build.xml	2017-03-28 14:04:41.946606996 +0200
@@ -290,13 +290,14 @@
            destdir="${build.dest}"
            source="${javac.source}"
            target="${javac.target}"
-           classpath="${build.dir}/classes:${tools.dir}/${jar.apis}:${tools.dir}/${jar.resolver}:${tools.dir}/${jar.serializer}"
+           classpath="${build.dir}/classes:${jar.jaxp}:${jar.apis-ext}:${jar.resolver}"
            debug="${debug}" nowarn="true"
            debuglevel="${debuglevel}"
            deprecation="${deprecation}"
            optimize="${optimize}"
            includeAntRuntime="false"
-           includeJavaRuntime="false"
+           includeJavaRuntime="true"
+           bootclasspath="${jar.jaxp}:${jar.apis-ext}:${jar.resolver}"
            excludes="org/xml/sax/** 
                 javax/xml/**
                 org/w3c/dom/*
@@ -1451,13 +1452,14 @@
                destdir="${build.dest}"
                source="${javac.source}"
                target="${javac.target}"
-               classpath="${build.dir}/classes:${tools.dir}/${jar.apis}:${tools.dir}/${jar.resolver}:${tools.dir}/${jar.serializer}"
+               classpath="${build.dir}/classes:${jar.jaxp}:${jar.apis-ext}:${jar.resolver}"
                debug="${debug}"
                debuglevel="${debuglevel}"
                deprecation="${deprecation}"
                optimize="${optimize}"
                includeAntRuntime="false"
-               includeJavaRuntime="false"
+               includeJavaRuntime="true"
+               bootclasspath="${jar.jaxp}:${jar.apis-ext}:${jar.resolver}"
                excludes="org/xml/sax/** 
                     javax/xml/**
                     org/w3c/dom/*
