Fermat's Library: software to help illuminate academic papers
fermatslibrary.com
fermatslibrary.com
As for the online part you may be conflating your point about offline annotation. Fermat's Library is about annotation sharing: implementing this functionality without any sort of identity management appears to me that it would basically be asking for trouble (imagine you could send e-mails to anyone without logging into anything).
It's easy to casually throw around phrases like "log in to a proprietary service" to criticise something. Perhaps that sentiment is understandable, but it doesn't really move the conversation forward or lead to better solutions. In this case I think it's just simply missing the point: at least at this point in time Fermat's Library's mission doesn't appear to be about grabbing your identity for profit. So unless there is something particularly fishy about what they are doing, that sort of criticism seems unfounded.
What would be the "first-party software" in that case?
Additionally, like many social sites, the idea is to collect user-created value for free, centred solely within their control. That aspect echoes of the great problem with scientific publishing: Scientists produce information, and give it away to some corporation for free, which then charges the public to access it. The user comments, even if informative, are stuck on the site; you have to return to the site to access those comments.
Even if "All team members have an academic background and share the desire to make science more open and widely distributed" [0], there is no guarantee that the user-populated database of annotations will remain free or accessible in the future, since again, it's stuck on that site.
That said I wish Fermat every success. Any way that helps you drink from the firehose of publications is a much needed step forward. Even if there is so much more you can still do in this respect...
I have no direct insight into the motivations of Fermat's Library but based on past interviews, the brothers Luís & João Batalha are 2 of the 4 founders and they said it's a side project and not meant to be a for-profit service. They're paying for server costs on their own. They also make the platform software (Margins) that Fermat's Library runs on free for other universities to use.
Their "day job" is a B2B sales marketing service which has nothing to do with science publishing: https://amplemarket.com/about
So the analogy would be Hacker News website being a "side project" of Paul Graham and YCombinator offering free access to some weblinks aggregation.
It's understandable that other commercial services that are paywalled make people distrust the future of a supposedly "free" service. I guess the same could have been said about Paul Graham back in 2007: "How do we know that PG won't paywall the HN website in the future and lock us all out of our free contributions of thread comments?"
Nobody but PG could have answered that hypothetical question and yet... here were are.
Yes, anything can happen and it's possible for the brothers to backtrack from their words but it would make them look bad for little gain. I think their intentional profit company Amplemarket has a better chance of making a lot of money than an academic annotation service. Perhaps we can use that in our Bayesian Probability of trusting/distrusting their future plans.