As promised, I'll describe my current writing framework. Please keep in mind that I came up to this only a few weeks ago, and can be highly improved/refined. It is centered on two main elements: plain text files and a wiki. For the most part, if not all, the tool used come from good practices in software development.
To start with, I ditched all fancy writing assisting software (described in the previous part) and returned to the basics with a text editor. There are many to choose from in different platforms, and I'm using Vim to do the job. In Windows a good alternative is Notepad++ but the old and simple Notepad will do. The reason behind this is to 1) be completely free of proprietary formats and lock-ins, 2) Focus on content leaving all issues regarding presentation and heavy formatting to a later step. Nevertheless, to introduce some basic formatting options while writing, I use Markdown syntax. Markdown is a simple markup language very easy to read and write which can be converted to valid HTML or other formats later.
Continuing with the workflow, since the files are simple text files they lend themselves to be easily tracked in versioning system/software. This allows to keep track of the changes the files suffer throughout the process and thus return to any previous point. Together with a service like github or bitbucket it can work as a backup solution. Bitbucket works particularly well since in the free tier it offers up to 5 private projects (or as called in the jargon "repositories") and is what I'm using.
The second principal element, the wiki system. I decided to use one to build some sort of database with characters, location, items, world building and so on. Each element can have an entry and I can link between them as I see fit. There should be some free wiki providers, among those are github and bitbucket. In most cases, wiki providers use one or another flavor of a markdown syntax to write on them, making an extra argument to write the content part also in markdown.
Since I touched on the topic of versioning and services offering it, I could also talk about other nifty tool provided by the software development world: tickets/issues. For now, I'm using them as reminders of details or decisions I have to make. Ends up being some sort of ToDo list or tasks. Also, I see them as a good tool when working with an editor to keep the corrections and commentaries in a coherent fashion. Probably a wiki could also be used in the same way. But again, a ticketing system (called in the jargon issues) is also provided by services like github/bitbucket.
An extra advantage of my workflow using bitbucket, is that I can work anywhere I want and in any platform. It is extremely portable and I'm sure it supports a lot of flexibility and improvements.