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/*
ue=''/>
<input type='submit' value='search'/>
</form>
</td></tr></table>
<div class='path'>path: <a href='/guix/log/?id=8feb56b0d4399dc93207a061ddb8582558d3b8cb'>root</a>/<a href='/guix/log/tests?id=8feb56b0d4399dc93207a061ddb8582558d3b8cb'>tests</a>/<a href='/guix/log/tests/guix-environment.sh?id=8feb56b0d4399dc93207a061ddb8582558d3b8cb'>guix-environment.sh</a></div><div class='content'><table class='list nowrap'><tr class='nohover'><th class='left'>Age</th><th class='left'>Commit message (<a href='/guix/log/tests/guix-environment.sh?id=8feb56b0d4399dc93207a061ddb8582558d3b8cb&amp;showmsg=1'>Expand</a>)</th><th class='left'>Author</th></tr>
<tr><td><span title='2016-07-26 17:59:25 +0200'>2016-07-26</span></td><td><a href='/guix/commit/tests/guix-environment.sh?id=201855221fa426851556b973e39f21e5ced7dfdf'>environment: Set 'GUIX_ENVIRONMENT' to the profile.</a><span class='msg-avail'>...<span class='msg-tooltip'>* guix/scripts/environment.scm (create-environment): Set
'GUIX_ENVIRONMENT' to PROFILE.
* tests/guix-environment.sh: Test it.
* doc/guix.texi (Invoking guix environment): Document it.
</span></span></td><td>Ludovic Courtès</td></tr>
<tr><td><span title='2016-06-05 00:05:38 +0200'>2016-06-05</span></td><td><a href='/guix/commit/tests/guix-environment.sh?id=40d71e44f5068b28f48bd131940260cc0ab2e2d1'>profiles: 'profile-derivation' now honors #:system.</a><span class='msg-avail'>...<span class='msg-tooltip'>Fixes &lt;http://bugs.gnu.org/23682&gt;.
Reported by Ander GM &lt;anthk@openmailbox.org&gt;.

* guix/profiles.scm (profile-derivation): Pass #:system to
'gexp-&gt;derivation'.
* tests/guix-environment.sh: Add 'guix environment -s' test.
</span></span></td><td>Ludovic Courtès</td></tr>
<tr><td><span title='2016-02-12 22:02:06 +0100'>2016-02-12</span></td><td><a href='/guix/commit/tests/guix-environment.sh?id=779aa003fbacbbcb6973f289b607d1d285009cec'>scripts: environment: Build environments as profiles.</a><span class='msg-avail'>...<span class='msg-tooltip'>Fixes &lt;http://bugs.gnu.org/19816&gt;.

* guix/scripts/environment.scm (evaluate-input-search-paths)
(build-inputs): Delete.
(evaluate-profile-search-paths, strip-input-name)
(package-or-package+output?, package-environment-inputs)
(build-environment, inputs-&gt;profile-derivations): New procedures.
(create-environment, show-search-paths, launch-environment)
(launch-environment/container): Replace 'inputs' argument
with 'profile' argument.
(package+propagated-inputs): Strip off names off of input tuples.
(options/resolve-packages): Handle input tuples that specify an output
in expressions.
(guix-environment): Convert inputs into a profile to use in the
environment.  Remove non-package inputs such as origins from
environment inputs.
* doc/guix.texi ("invoking guix environment"): Document package+output
tuples for --expression option.
* tests/guix-environment.sh: Update tests.
* tests/guix-environment-container.sh: Likewise.

Co-authored-by: Ludovic Courtès &lt;ludo@gnu.org&gt;
</span></span></td><td>David Thompson</td></tr>