I see that LibreJS is blocking Trisquel's javascript.
I assume it failed the test because the JS file does not use the explicit license comments.
This could be a problem for many Drupal-based sites (such as Trisquel.info) because Drupal has a core functionality that aggregates all javascript files that are part of the site. This includes the core JS files, theme JS, module JS. Basically everything that is on the same server and referenced in code. External JS files are not included.
All the JS that is part of Drupal's core or modules/themes on drupal.org must be GPL-compatible. I make this claim because Drupal itself is GPL and all modules/themes uploaded there must be too (http://drupal.org/licensing/faq#q7). Therefore, all JS distributed with Drupal and those modules must at least be GPL-compatible.
Modules that are custom developed (and not publicly available) or that require external resources might not be Free.
Aggregating JS is an important optimisation because it can massively reduce the number of separate JS files to be loaded. However, assuming that all the JS files have the required license comment, that one file can possibly contain a mix of free and non-free licenses. I have only briefly looked at the Javascript Trap so I am not 100% sure of the rules and the desired/expected behaviour (I will do some research soon), but is killing the entire site's javascript the correct thing to do if the non-free code is not actually needed for using the site? Example, maybe the non-free code is used for a specific functionality like a gallery. If the JS files stay separate you could just remove the non-free code, but if it gets aggregated everything is removed.
I'd imagine that it would be somewhat difficult to remove non-free code from the file so it is probably easier/safer to just remove it entirely. This would be a good way to push the developers to do something about their JS code.
The problem with Drupal seems to have been picked up before: http://microblog.ourcoffs.org.au/notice/101133.
Besides this issue, good work on this addon. It will come in very handy once it becomes stable and refined.
I've added myself to the mailing list. I might be able to help test with Drupal-related issues.
