Eclipse classpath ordering - project dependency always at the bottom of dependencies

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Perhaps you could approach this another way and instead tweak the jar to remove the offending class file. Then you wouldn’t need to rely on classpath ordering.

configurations {
   commonsConfig { transitive = false }
}
dependencies {
    commonsConfig "commons-config:commons-config:1.10"
    compile files("$buildDir/tweaked-commons-config.jar")
}
task tweakCommonsConfig(type:Jar) {
   from zipTree(configurations.commonsConfig.singleFile).matching {
      exclude 'path/to/some.class'
   }
   destinationDir buildDir
   archiveName 'tweaked-commons-config.jar'
}
compileJava.dependsOn tweakCommonsConfig
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