To what extent should a reader be required to read a paper to understand a chapter? I am doing a master thesis and have more or less written my report. My supervisor has from time to time read my paper and from the feedback I get she wants to be able to skip to a later chapter and read it without necessarily reading exactly everything else before. This seems a bit odd to me, but I have not thought about it before as the papers I've read I read from the introduction and onwards.

My outline is introduction, related work, method, results, discussion, conclusion.

So, to what extent should I expect/force a reader to read previous chapters that are relevant but not critical for understanding the paper? Should the method chapter be written in a way that you don't have to read the related work and introduction chapter? Should you be able to skip to the results and discussion and understand them without reading the method chapter?
The flow of thesis differs in preference from one supervisor to another. The specification provided by your supervisor doesn't seem unreasonable. In fact, I would endorse it myself. 

It is natural for most readers to skip the introduction and just cut to the chase. Readers would be particularly interested in the implementation and results. Although that doesn't mean introduction isn't mandatory. You just have to minimise the dependency between the main matter and the introductory matter. The lesser you make the reader to turn back pages, the better would be the reading experience.