You are using the implementation class of the plugins (ex: com.netflix.gradle.plugins.rpm.RpmPlugin) as the ID. The ID of that particular plugin is nebula.rpm.
However, you do need to use the implementation class, not the ID, in an init script. In order to do that, you should remove the quotes around the implementation classes:
allprojects {
apply plugin: com.netflix.gradle.plugins.rpm.RpmPlugin
apply plugin: com.github.jengelman.gradle.plugins.shadow.ShadowPlugin
apply plugin: com.selesse.gradle.git.changelog.GitLogPlugin
}