Improve handling of references

Right now we treat some of the references (mostly papers) not very uniformly:

1. sometimes they are inlined in the theorem/conjecture description while sometimes mentioned on top.
2. When the same reference is mentioned in two different files, we have no mechanism to deduplicate the information.
3. There is no uniform format for citations: sometimes the first names are mentioned, the styling and order of the different parts of a citation are non handled consistently.
4. no consistent links to where one can obtain the

A solution to these shortcomings should take into account the limitations of doc-gen and make it convenient for both the reader of the source files and the output generated by doc-gen to access these citation with ease.