JIRA is in startup mode after I used the windows disk cleanup utility, defragmented the host it runs on, and rebooted. Previous to that the host had run out of space and was generating errors like "com.atlassian.jira.index.IndexingFailureException: Indexing completed with 1 errors" when a change was made.
The dbconfig.xml file seems to be missing and JIRA was using the default h2db so I think I need to regenerate that file and connect to it, but I can't find instructions on how to that.