This appears to be a known issue with Eclipse [1]. Perhaps there is something that JBoss Tools can do to override or fix this?

Only the minified version[2] shows an error, the normal non-minified version [3] does not show this behavior

[1] http://stackoverflow.com/questions/4282448/change-eclipse-settings-to-ignore-errors-on-a-specific-file
[2] http://code.jquery.com/jquery-1.6.4.min.js
[3] http://code.jquery.com/jquery-1.6.4.js

I was not sure what component to set - perhaps we need one for HTML/JS/CSS?