project and bin folders being created even when excluded

I am working on a project that has gradle build files in it, however those build files are not directly built in the project, and just stored there for distribution. However, the java plugin it still creating the .project and bin/.project files even if I have the following settings set in my settings.json file. (/resources) is where my files are.

    "java.import.gradle.enabled": false,
    "java.import.maven.enabled": false,
    "java.import.exclusions": [
        "**/node_modules/**",
        "**/.metadata/**",
        "**/archetype-resources/**",
        "**/META-INF/maven/**",
        "**/resources/**"
    ],
    "java.configuration.updateBuildConfiguration": "disabled"

There needs to be a way to completely disable the plugin from the settings so we don't get those files created on any repo that contains a build.gradle file.