Documentation for JIRA 5.1.x. Documentation for other versions of JIRA is available too. 
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hsql stores its database in text files on the filesystem. Typically these will be in a database subdirectory of your JIRA Home Directory:
[jira-home-directory ~]$ ls -l database/ total 108 -rw-r--r-- 1 jturner jturner 0 Jul 28 09:12 jiradb.data -rw-r--r-- 1 jturner jturner 343 Jul 28 09:12 jiradb.properties -rw-r--r-- 1 jturner jturner 72272 Jul 28 10:02 jiradb.script [jira-home-directory ~]$
The hsqldb binary is usually located in the lib sub-directory of your JIRA Installation Directory:
[jira-installation-directory ~]$ ls lib/hsql* lib/hsqldb-1.8.0.5.jar
If you haven't already, shut down any apps using the database.
Run the following command from the directory that contains the database directory (JIRA 4.0+):
java -cp lib/hsqldb-1.8.0.5.jar org.hsqldb.util.DatabaseManager -user sa -url jdbc:hsqldb:database/jiradb
In versions of JIRA before JIRA 4.1 the jar file was in common/lib
The hsqldb console should load, listing tables in the database in the left panel. You can run SQL commands in the top panel:
Once you have finished running SQL queries, shut down the console before starting JIRA/Confluence.