It seems that index subdirectories aren't being created properly. I store indexes in:
/export/home/orion/jira-index/
which exists, and I manually created the 'issues' directory to try and fix the problem, but sub-directories aren't getting created. Here's a stack trace:

2002-08-15 09:33:03,652 ERROR [atlassian.jira.search.DefaultIndexManager] Problem with path /export/home/orion/jira-index/issues: /export/home/orion/jira-index/issues/segments (No such file or directory)
java.io.FileNotFoundException: /export/home/orion/jira-index/issues/segments (No such file or directory)
at java.io.RandomAccessFile.open(Native Method)
at java.io.RandomAccessFile.<init>(RandomAccessFile.java:93)
at java.io.RandomAccessFile.<init>(RandomAccessFile.java:138)
at org.apache.lucene.store.FSInputStream$Descriptor.<init>(Unknown Source)
at org.apache.lucene.store.FSInputStream.<init>(Unknown Source)
at org.apache.lucene.store.FSDirectory.openFile(Unknown Source)
at org.apache.lucene.index.SegmentInfos.read(Unknown Source)
at org.apache.lucene.index.IndexReader$1.doBody(Unknown Source)
at org.apache.lucene.store.Lock$With.run(Unknown Source)
at org.apache.lucene.index.IndexReader.open(Unknown Source)
at org.apache.lucene.index.IndexReader.open(Unknown Source)
at com.atlassian.jira.search.DefaultIndexManager.getIssueIndexReader(Unknown Source)
at com.atlassian.jira.search.DefaultIndexManager.reIndex(Unknown Source)
at com.atlassian.jira.event.listeners.search.IssueIndexListener.reIndex(Unknown Source)
at com.atlassian.jira.event.listeners.search.IssueIndexListener.issueClosed(Unknown Source)
at com.atlassian.jira.event.issue.IssueEventDispatcher.dispatchEvent(Unknown Source)
at com.atlassian.jira.event.issue.IssueEventDispatcher.dispatchEvent(Unknown Source)
at com.atlassian.jira.event.issue.IssueEventDispatcher.dispatchEvent(Unknown Source)
at com.atlassian.jira.issue.managers.DefaultIssueManager.resolveCloseIssue(Unknown Source)
at com.atlassian.jira.web.action.issue.ResolveIssue.doExecute(Unknown Source)
at webwork.action.ActionSupport.execute(ActionSupport.java:108)
at webwork.dispatcher.ServletDispatcher.service(ServletDispatcher.java:220)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:336)
at com.evermind._eab.doFilter(Unknown Source)
at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(Unknown Source)
at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(Unknown Source)
at com.evermind._dzb.doFilter(Unknown Source)
at com.atlassian.jira.web.security.SecurityFilter.doFilter(Unknown Source)
at com.evermind._dzb.doFilter(Unknown Source)
at com.atlassian.jira.web.security.LoginFilter.doFilter(Unknown Source)
at com.evermind._cxb._abe(Unknown Source)
at com.evermind._cxb._uec(Unknown Source)
at com.evermind._io._twc(Unknown Source)
at com.evermind._io._gc(Unknown Source)
at com.evermind._if.run(Unknown Source)
2002-08-15 09:33:03,668 ERROR [event.listeners.search.IssueIndexListener] Error re-indexing Issue[GenericEntity:Issue][project,10000][type,3][created,2002-08-08 09:58:35.274][summary,finalise tools server][votes,0][component,null][timeestimate,0][id,10016][status,6][resolution,1][description,Need Ops to sort out where the server is going, and once they have, get a new Perforce license and check everything is OK.][reporter,robeq1][updated,2002-08-15 09:33:03.356][assignee,robeq1][priority,2][environment,][fixfor,10000][timespent,null][key,TLS-9]