So you've got a development instance of Confluence running using the Atlassian SDK & atlas-run, but now want to access the database with some kind of GUI. How?
Easy. First shutdown the Confluence instance – CTRL+C should do the trick.
From the base directory of your plugin add-on:
magical-addon$ ls
pom.xml src target
magical-addon$ java -cp ./target/confluence/webapp/WEB-INF/lib/hsqldb-2.3.0.jar org.hsqldb.util.DatabaseManager -user sa -url jdbc:hsqldb:./target/confluence/home/database/confluencedb
This will bring up the HSQL Database Manager from which you can use SQL to delve deeper:
On JIRA
For JIRA (6.1), the command is
java -cp ./target/jira/webapp/WEB-INF/lib/hsqldb-1.8.0.5.jar org.hsqldb.util.DatabaseManager -user sa -url jdbc:hsqldb:./target/jira/home/database
Note that versions of the HSQL jar will change, and that the name and location of the confluencedb.script and database.script file