Academic writing software General-purpose word-processing programs are OK for academic writing. But I feel the experience can be much improved with some specialized software that takes better care of the special needs of academic writers, such as version control, collaboration, reference generation, in-text citation etc.

Is there any such software (either web-based or desktop-based) created specifically for academic writers?
First of all, academic writing is all about the mind putting words on paper, you are really looking for tools to help you with the technical side of putting together the material. Looking at your list of examples, I do not see much that is not already implemented in Word (probably being the most common writing tool in academia). A second that contains everything except a solid version control (revision tool) is (La)TeX (which is also free). But, if version control is required you can use GitHub, as I know many LaTeX authors do.

On a more personal side, the difficulty in writing science is not about getting the technical aspects right, it may be tedious and boring but is easily done. What matters is the text and how to be precise and concise and no software will help you there. Version control is sometimes a good tool but really, is it necessary to see everything one has written and deleted? Isn't the present text what really matters and what one has to consider for improvements? It is easy to get bogged down with the wrong details so getting tools to sort those out is never wrong but I do not necessarily see how a special purpose academic writing tool will help much more than with the technicalities than existing tools do.