I have a custom war file with some custom modules that we are using for our website. I want to use MySQL as our content repo and maintain the data in the repo across new war file deployments to tomcat. Hovever, whenever I try to deploy a new war, I get java errors during magnolia startup. Here is the first one (al are similar referring to indexing the repo):

2010-12-20 09:58:31,841 ERROR org.apache.jackrabbit.core.RepositoryImpl : Unable to initialize workspace 'website'
javax.jcr.RepositoryException: Error indexing workspace
at org.apache.jackrabbit.core.SearchManager.initializeQueryHandler(SearchManager.java:540)
at org.apache.jackrabbit.core.SearchManager.<init>(SearchManager.java:213)
at org.apache.jackrabbit.core.RepositoryImpl$WorkspaceInfo.getSearchManager(RepositoryImpl.java:1790)
at org.apache.jackrabbit.core.RepositoryImpl$WorkspaceInfo.doPostInitialize(RepositoryImpl.java:2008)
at org.apache.jackrabbit.core.RepositoryImpl$WorkspaceInfo.initialize(RepositoryImpl.java:1921)
at org.apache.jackrabbit.core.RepositoryImpl.getWorkspaceInfo(RepositoryImpl.java:735)
at org.apache.jackrabbit.core.RepositoryImpl.login(RepositoryImpl.java:1377)
at org.apache.jackrabbit.core.jndi.BindableRepository.login(BindableRepository.java:162)
at info.magnolia.cms.util.WorkspaceAccessUtil.createRepositorySession(WorkspaceAccessUtil.java:123)
at info.magnolia.cms.beans.config.ContentRepository.registerNameSpacesAndNodeTypes(ContentRepository.java:390)
at info.magnolia.cms.beans.config.ContentRepository.loadRepository(ContentRepository.java:359)
at info.magnolia.cms.beans.config.ContentRepository.loadRepositories(ContentRepository.java:314)
at info.magnolia.cms.beans.config.ContentRepository.init(ContentRepository.java:189)
at info.magnolia.cms.beans.config.ConfigLoader.load(ConfigLoader.java:102)
at info.magnolia.cms.servlets.MgnlServletContextListener$2.doExec(MgnlServletContextListener.java:207)
at info.magnolia.context.MgnlContext$VoidOp.exec(MgnlContext.java:434)
at info.magnolia.context.MgnlContext$VoidOp.exec(MgnlContext.java:432)
at info.magnolia.context.MgnlContext.doInSystemContext(MgnlContext.java:396)
at info.magnolia.cms.servlets.MgnlServletContextListener.startServer(MgnlServletContextListener.java:205)
at info.magnolia.cms.servlets.MgnlServletContextListener.contextInitialized(MgnlServletContextListener.java:201)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4135)
at org.apache.catalina.core.StandardContext.start(StandardContext.java:4630)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:791)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:771)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:546)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:905)
at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:525)
at org.apache.catalina.startup.HostConfig.check(HostConfig.java:1359)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.apache.tomcat.util.modeler.BaseModelMBean.invoke(BaseModelMBean.java:297)
at com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.invoke(DefaultMBeanServerInterceptor.java:836)
at com.sun.jmx.mbeanserver.JmxMBeanServer.invoke(JmxMBeanServer.java:761)
at org.apache.catalina.manager.ManagerServlet.check(ManagerServlet.java:1500)
at org.apache.catalina.manager.HTMLManagerServlet.doPost(HTMLManagerServlet.java:252)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:637)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:563)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:298)
at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:857)
at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:588)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489)
at java.lang.Thread.run(Thread.java:680)
Caused by: java.io.IOException: Error indexing workspace
at org.apache.jackrabbit.core.query.lucene.MultiIndex.createInitialIndex(MultiIndex.java:382)
at org.apache.jackrabbit.core.query.lucene.SearchIndex.doInit(SearchIndex.java:511)
at org.apache.jackrabbit.core.query.AbstractQueryHandler.init(AbstractQueryHandler.java:66)
at org.apache.jackrabbit.core.SearchManager.initializeQueryHandler(SearchManager.java:538)
... 51 more
Caused by: org.apache.jackrabbit.core.state.NoSuchItemStateException: 997b2ee7-8d2b-40f0-812d-16f552825b00
at org.apache.jackrabbit.core.state.SharedItemStateManager.getItemState(SharedItemStateManager.java:270)
at org.apache.jackrabbit.core.query.lucene.MultiIndex.createIndex(MultiIndex.java:1102)
at org.apache.jackrabbit.core.query.lucene.MultiIndex.createInitialIndex(MultiIndex.java:375)
... 54 more

Recreating the Magnolia (blank) schema corrects the problem, but of course we want to keep the content of the db across war deployments. Is this possible?