Hi,

I just installed and started to use your plugin but I quickly discovered it was messing with the formatting on some pages even tho I don’t use the shortcode on those.

So I took look at the code and saw this:

remove_filter( 'the_content', 'wpautop' );
add_filter('the_content', 'wpautop' , 99);
add_filter('the_content', 'shortcode_unautop',100 );

So that means a lot of things that didn’t go through wpautop before are now being reformatted. That includes every shortcodes.

There’s a much better solution that I found here: https://bit.ly/1LM05R1 and that inspired me to find a much better solution. Here’s the modified markdown_shortcode.php that I am using:

include('parsedown/Parsedown.php');
include('parsedown/ParsedownExtra.php');

$markdown_shortcode_content = array();

function markdown_shortcode($attr, $content = null) {
    global $markdown_shortcode_content;
    $content = $markdown_shortcode_content[$content];

    $content = undo_html_entities($content);
    $content = trim($content);
    $content = underscores_to_spaces($content);

    $extra = new ParsedownExtra();
    $parsed_content = $extra->text($content);

    return $parsed_content;
}
add_shortcode('markdown', 'markdown_shortcode');

function markdown_shortcode_pre($attr, $content = null) {
    global $markdown_shortcode_content;
    $key = md5($content);
    $markdown_shortcode_content[$key] = $content;
    return "[markdown]{$key}[/markdown]";
}

function markdown_shortcode_preprocess($content) {
    global $shortcode_tags;

    // Backup current registered shortcodes and clear them all out
    $orig_shortcode_tags = $shortcode_tags;
    $shortcode_tags = array();

    add_shortcode('markdown', 'markdown_shortcode_pre');

    // Do the shortcode (only the one above is registered)
    $content = do_shortcode($content);

    // Put the original shortcodes back
    $shortcode_tags = $orig_shortcode_tags;
    return $content;
}
add_filter('the_content', 'markdown_shortcode_preprocess', 1);

// Reverts changes that were applied by the Visual editor
function undo_html_entities($content){
    $content = str_replace("<", "<", $content);
    $content = str_replace(">", ">", $content);
    $content = str_replace("&", "&", $content);
    return $content;
}

// Replaces more than one underscore to same amount of spaces
function underscores_to_spaces($content) {
    $content = preg_replace_callback('/_{2,}/', function ($matches) {
        return str_replace('_', ' ', $matches[0]);
    }, $content);
    return $content;
}

function init_highlight() {
    wp_enqueue_style("highlight",  plugin_dir_url(__FILE__) . 'highlight/styles/github.css');
    wp_enqueue_script("highlight",  plugin_dir_url(__FILE__) . 'highlight/highlight.min.js');
    wp_enqueue_script("highlight_init",  plugin_dir_url(__FILE__) . 'init_highlight.js');
}
add_action('init', 'init_highlight');

Also, I don’t know why you added that last part, the code doesn’t tell but I think you should at least document that side effect or just don’t do it if you can avoid it (I removed it).

// Stop WordPress converting quotes to pretty quotes (nobody will miss them)
remove_filter('the_content', 'wptexturize');

also, you should prefix all your methods with a unique prefix or use an object because you’re going to create conflicts.

Hope that helps