Scrivener is a pretty amazing piece of software. Its genesis was for writing novels, but it is well suited to academic writing as well. Its reference section and cork board are nice to have, and allow one to view reference material while writing in an adjacent pane of the editor.

https://www.literatureandlatte.com

http://www.inkitpub.com/2016/08/16/scrivener-author-dashboard/

https://danielvreeman.com/using-scrivener-for-writing-scientific-papers/

https://alawuntoherself.com/2015/10/20/how-i-use-scrivener-for-academic-writing/

http://www.academicpkm.org/2013/11/19/using-scrivener-complex-academic-writing-projects/

http://thedigitalresearcher.com/managing-your-edits-with-scrivener-snapshots/

http://lifehacker.com/how-scrivener-helped-me-organize-all-my-writing-1599446028

https://www.literatureandlatte.com/forum/viewforum.php?f=19

https://tacet.wordpress.com/2014/06/02/using-scrivener-to-write-a-dissertation-why-im-glad-i-did-and-what-i-would-do-differently-next-time/

http://www.chronicle.com/blogs/profhacker/scrivener-scrivening-scriverastic/23026