Given the limitations of Gradle's EclipseClasspath
API, the most straightforward solution I can think of is to declare src/main/conf
as another source directory:
sourceSets.main.java.srcDir "src/main/conf"
As long as the directory doesn't contain any Java files, this won't affect the outcome of the Gradle build. However, the directory will show up as a source directory in Eclipse, and its properties files will therefore be copied into the Eclipse output directory.