Reply To: What is the best organising system?

Having learnt HTML about 15 years ago (and added CSS to it along the way) it is very difficult for me to “unlearn” it and give you advice on where to start. I have no experience whatever of Muse, though I have watched a couple of videos about it by Terry White. I think I would begin by exploring the Export as HTML option within InDesign and see whether that gives you any satisfaction. Try exporting a few pages, open them in a web browser and see whether you are horrified by the result.

So far as learning HTML goes, I found Elizabeth Castro’s “HTML for the World Wide Web” (one of the Visual Quickstart series of books) very helpful. I think the latest edition is the 5th.

I don’t see 100000 words as a barrier since each of your chapters could be a separate page of HTML with links between them. Indeed, there is no limit to how many pages you can have, provided there are links between them. For instance, ask yourself how many words there are in Wikipedia! Each of your chapters might have multiple pages.

Without actually seeing your thesis, I feel that I am simply tossing ideas at it in the dark without any real knowledge of whether any of them are hitting the mark. Maybe someone else can offer more knowledgeable suggestions?