Aloha copy contextual links when editing a block

On my copy (using omega theme) the contextual links are not in the same block as the content. Perhaps your theme doesn't make the separation between block links and content?

The place to fix this would be in the module's aloha.js

Somewhere in

    // Strip our span target and any following tags from content to be saved.
    getContentFromContainer: function(container) {
      var $containerClone = jQuery(container).clone();
      $containerClone.find('.aloha-target, .aloha-target ~ *').remove();
      return $containerClone.html();
    },

we could add another line which removes any known tags we don't want to be added to the content. I've got a feeling this should be initialised as a setting something like
Drupal.settings.aloha.removedTags = ['.contextual-links']
so that site builders can add to this setting if they have other tags that also need to be stripped.

Ok, have just pushed an update which should enable this. From the documentation added to the README

Certain elements need to be removed from the content before being sent back to
the server to be saved. These include the aloha target spans themselves, any
elements added after the aloha target spans (eg context can add target links to
the content area) and contextual links (dependent upon your theme).
If you need to remove other elements you may override
Drupal.settings.alohaElementsToStrip
which is a simple jQuery selector string listing the elements to be removed.
It defaults to
Drupal.settings.alohaElementsToStrip = '.aloha-target, .aloha-target ~ *, .contextual-links-wrapper'
so remember to include these in your override.
You should be able to override this from within a module or from your theme js.

Bit annoying having to add a new namespace within settings, but if we tried to use something like Drupal.settings.aloha.elementsToStrip then it gets zapped when the module adds the aloha settings. So in order to keep the code visible within the js file we need to add a new namespace.

If you could check whether this works for you with your original theme that would be great. Should be available from git now, and from the dev tarball after the next packaging.

Marking this one as fixed. Please reopen if you are still experiencing issues with the latest release.