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example that classLoader is for loading other classes, not a Checker itself.

    /** Class loader to resolve classes with. **/
    private ClassLoader classLoader = Thread.currentThread()
            .getContextClassLoader();

    /**
     * Sets the classloader that is used to contextualize fileset checks.
     * Some Check implementations will use that classloader to improve the
     * quality of their reports, e.g. to load a class and then analyze it via
     * reflection.
     * @param classLoader the new classloader
     */
    public final void setClassLoader(ClassLoader classLoader) {
        this.classLoader = classLoader;
    }

vs

    /** The classloader used for loading Checkstyle module classes. */
    private ClassLoader moduleClassLoader;

Checker.setClassLoader is required only for JavadocMethodCheck (by mean of AbstractTypeAwareCheck) both classes are deprecated.
If we remove Checker.setClassLoader, we will damage work of JavadocMethodCheck class so we should remove this method only after we re-implement this Check.

So it mean that introduction of new API method only in satisfy deprecated functionality is NOT OK.

@rnveach , see comment above, so it is not ok to change API to support deprecated functionality.
It is not OK to allow any other RootModule to think that classLoader is required.

classLoader is optional.
It will exists in Checker (default RootModule) till we reimplement JavadocMethodCheck to use grammar.

For now, I recommend to do a workaround in our ANT task to check name of RootModule and if it is Checker do cast and do setClassLoader. So we will support JavadocMethodCheck only in Checker.
If user do like this, he need to make its own AntTask class.