In the openrdf-http-server-servlet.xml file the adunaAppConfig bean (class: info.aduna.app.AppConfiguration) can accept a dataDir property with the value of the data-directory.
I haven't found this documented anywhere, so I hope this helps someone. Probably that person will be me next time I need to configure Sesame.
The fragment in question:
<bean class="info.aduna.app.AppConfiguration"
destroy-method="destroy" id="adunaAppConfig"
init-method="init">
<property name="applicationId" value="OpenRDF Sesame">
<property name="longName" value="OpenRDF Sesame">
<property name="version" ref="adunaAppVersion">
<property name="dataDirName" value="/var/lib/aduna">
</bean>