Skinr indiscriminately adds contextual-links class to skinr theme_hook elements even when no skins are available

Also, while skinr adds the contextual_links class to these problematic elements I never see a cogwheel appear in the corner of these elements. Even when I make my skins available to the html and region theme hooks. Maybe the contextual links module does not support it?

This is most likely due to the missing $title_prefix and $title_suffix variables in the region template. Drupal thinks it's going to have contextual links (so outputs the contextual_links class), but then can't add the actual contextual links.

Skinr UI doesn't actually add the classes, drupal core does, as soon as it detect a contextual link.
But we can definitely test for the availability of skins that apply to body or regions (from memory, I believe that includes: * (or all), html, region-*)

Perhaps, instead we should try fix the CSS that makes the contextual_links class misbehave? Or would that be too drastic?

skinr_ui_preprocess() is where the contextual links get added (there are some exception for views and panels, if I remember correctly).
skinr_get_skin_info() will return an array with available skin plugins.

If you want to test whether or not a skin plugin is enabled on the site:

<?php
  // Apply overridden status to skins.
  $skin_infos = skinr_get_skin_info();
  foreach ($skin_infos as $skin_name => $skin_info) {
    $skin_infos[$skin_name]['status'] = skinr_skin_info_status_get($skin_infos[$skin_name]);
  }
?>

The 'theme hooks' property of a skin plugin determines whether or not a skin is allowed to be used for a particular theme.

_skinr_is_featured() might be useful (or it might not).

Some suggestions:

if (is_array($skin_infos[$skin_name]['theme hooks']) && isset($skin_infos[$skin_name]['status'][$theme]) && $skin_infos[$skin_name]['status'][$theme]) { can be replaced with a simple (and much faster) if (is_array(!empty($skin_infos[$skin_name]['status'][$theme])) {. is_array() is a very slow function, and empty fails without throwing an error if $skin_infos is not an array.

Add some caching to your new function; it'll be called many times, once for each theme hook. It looks like you were planning to do it, but forgot.

Instead of $skinnable_hooks[] = $active_hook; try $skinnable_hooks[$active_hook] = $active_hook;. You can then use if (isset($skinnable_hooks[$hook])) { instead of if (!in_array($hook, $skinnable_hooks)) { in skinr_ui_preprocess(), which should be much faster.

Also, why did you remove the previously added 'fix' for the HTML element? If a skin is available for it, that problem still exists... or is it not a good one?

The caching should cache the settings per theme, then you can check which theme is current and pull cached settings for just that theme.
Another note: we shouldn't use the global $theme variable. Use skinr_current_theme() instead. If there's an issue with using that function, that means there's a bug and it should be fixed, instead of circumventing it here.

<?php
function skinr_get_skinnable_hooks() {
$skinnable_hooks = &drupal_static(__FUNCTION__, array());

$theme = skinr_current_theme();
if (!isset($skinnable_hooks[$theme])) {
// ...
?>

I'm seeing static cache, but no per-theme caching. Also, it's still using in_array().

This patch will probably fail test (they would have to be updated; also a test specific to skinable hooks functionality would have to be added).
I fixed it up to work properly.

The question is, is this really effective considering most skins will have theme hooks set to '*', which applies to any hook?

Also, this really doesn't solve the ticket's issue, just makes it not show up under some very specific circumstances.

We need working tests, then we can commit the patch.

Even though you already know, I can confirm that the patch in #16 fixes my having contextual links everywhere displaying all the time.

Although a side effect seems to be that I now have no skinr contextual links anywhere ever. Even when something has a skin.
Makes it a bit hard to administer.

[Edit] This is because in my skin definition I had:

    'theme hooks' => array('node__my_type'),

But for contextual links to show I have to have:

    'theme hooks' => array('node', 'node__my_type'),

But I don't actually want this skin to be available on all node types so adding 'node' to theme hooks is not a good solution for me.

As rooby mentioned, besides the test, this patch needs some work. As it stands right now it only works with base theme hooks (like node, or block), not with derivates (like node__page or block__system).

I added tests and fixed the problems with that patch. New patch attached.
Also, committed.