After the changes committed in https://www.drupal.org/node/2367069#comment-9308523, changes to a link made through hook_preprocess_link() are not working anymore.

I came across this when using ctools_automodal, which uses a hook_preprocess_link() to add classes and to alter the url in the link (see https://github.com/wojtha/ctools_automodal/blob/prefixed_hooks/ctools_au...). After applying the patch mentioned above, the classes aren't being added, and the url isn't altered in the final output (when I dsm() the $variables array at the end of ctools_automodal_preprocess_link(), everything is where it should be.

Not sure whether Link module or ctools_automodal is responsible for this.

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brunodbo created an issue.