Problem

Confluence fails to rebuild indices. The log contains warning messages like the following:

WARN [confluence-interactive-reindexing-thread] [atlassian.bonnie.index.BaseMultiThreadedIndexer] reindex Timed out while waiting for reindexing threads to terminate. Continuing to wait...

Cause

There is a misconfigured confluence.cfg.xml.

Resolution

Edit <confluence-home>/confluence.cfg.xml. Review the datasource and confirm that it points to the correct datasource rather than (for example) the datasource defined for JIRA user integration.