Have you considered using Bookdown? It is package for the R language (best known for data munching and statistics) that can generate PDF/ LaTex/ HTML/ e-Pub etc from a single Markdown text file. It has markdown syntax extensions for citations and bibliography. You will need a mac or PC (Windows or Linux) to run R-Studio to generate the actual output, but the input files are plain text, so can be edited with any iOS text editor. I put them in Dropbox for cross platform access, but iCloud should be fine for a pure Apple solution, and edit them with Byword.