This is related to CORE-2164.
The attached project contains a single test which uses SpringLiquibase to execute changelogs inside a jar. One of those changelogs includesAll other changelogs inside the "extra" directory within the jar. This works in 3.0.0 but causes the following exception in 3.3.1:
The test can be executed with "mvn install".
Java(TM) SE Runtime Environment (build 1.6.0_45-b06)