Losing your Database
If you find yourself 'losing' your collections after restarting Tomcat adjust the location of your database to be somewhere other than the webapps directory ! This is achieved by editing the WEB-INF/system.xml
<root-collection dbroot="/var/xmldb/db" name="db" use-metadata="on">
this will store the data in a directory you have created /var/xmldb/db.