It also speaks volumes when a company would rather direct resources towards litigation instead of innovation. Engineers tend to be cheaper than lawyers and legal maneuvering will only delay the demise of an inferior product temporarily.
I just downloaded Zotero in response to this lawsuit. It's good stuff, very handy and minimally obtrusive, but plenty of functionality when you want it. That's the way to make software these days: minimal learning curve, and fitting into people's pre-existing habits.
The linked article said that GMU was sued for violating its license agreement with EndNote. So, this isn't the same question as whether or not a third party app may read/write MSOffice file formats. If an organization signs a license agreement stating that all users of data aggregated by Product A must access that data via a licensed copy of that product but instead issues some of its employees Product B which reads Product A's data, isn't that a legitimate license violation? I probably wouldn't enter into such an agreement as a customer, but one could conceivably do so. We don't actually know from the article what the case was about or what the judges ruled upon.
It is impossible to 'unlicense' the right to reverse engineer. (if you reverse engineer only to support another company's format.). If i'm wrong on this one, let me know.
The case could have addressed some interesting questions, such as the degree to which duplicating functionality falls under the definition of reverse engineering, and whether a file-format translator is a derivative work, as well as whether it's legally permissible to prohibit either of these.
Have these questions not been addressed before in court?
It is great advertising for the other company, even if you do win.