pre_get_posts: targeting the right query

[cheh]

I want you to pay attention that pre_get_posts action in your plugin has an effect on all queries:

add_action('pre_get_posts', 'commentnavi_allcomments');
function commentnavi_allcomments() {
	if (intval(get_query_var('comment-all')) == 1) {
		set_query_var('comments_per_page', 9999);
	}
}

And it throws some unexpected behavior and/or conflicts with other plugins, e.g. https://wordpress.org/support/topic/backend-error-since-version-1-6-4-1/

I'm pretty sure that you should add a couple of conditional tags to target the right query:

add_action('pre_get_posts', 'commentnavi_allcomments');
function commentnavi_allcomments() {
	if ( ! is_admin() && is_main_query() && intval(get_query_var('comment-all')) == 1) {
		set_query_var('comments_per_page', 9999);
	}
}

More information here.