A .jar added to the Eclipse classpath is missing at runtime

Yes, in the previous releases the compile classpath was equal to the runtime classpath.

You can disable the runtime classpath filtering by removing the corresponding classpath attribute from the dependency.

eclipse.classpath.file.whenMerged {
    entries.each { 
        if (it.path.contains("com.example.parser")) {
            it.entryAttributes.remove("gradle_used_by_scope")
        }
    }
}