I've just upgraded my spring boot version from 1.0.4.RELEASE to 1.1.5.RELEASE and think I may have found an issue that extends https://github.com/spring-projects/spring-boot/issues/672 and https://github.com/spring-projects/spring-boot/issues/1215. I have a multi-project gradle build, my main application includes some of the other projects as dependencies using: ``` groovy compile project(':myapplication-common') ``` The "myapplication-common" project includes filesystem dependencies: ``` groovy compile files {"lib/myExternalJar-1.1.jar"} ``` Following the upgrade this filesystem based transitive dependency is no longer bundled in the boot jar, prior to the upgrade it was. For now I'm using the following workaround in the main app gradle file: ``` groovy compile files {"../myapplication-common/lib/myExternalJar-1.1.jar"} ``` With this workaround in place the dependency is bundled.