I tried to start SQUirrel 3.1 but I received a message stating "Could not find the main class Files\Rational\ClearQuest\cqjni.jar" I noticed that C:\Program Files\Rational\ClearQuest\cqjni.jar is in my existing classpath as defined by the Windows environment variable, CLASSPATH.
SQUirrel doesn't need my existing classpath, so I updated the SQUirrel bat file, squirrel-sql.bat.
REM SET SQUIRREL_CP=%TMP_CP%;%CLASSPATH%
SET SQUIRREL_CP=%TMP_CP%
It no longer appends my existing classpath to its classpath and runs fine.