How to manage the structure of a masters thesis and what mistakes to look out for? I'm writing my master thesis at the moment in the area of cyber/computer security.
However, I'm having real trouble in keeping a good structure in the thesis.

What I mean with structure is that my supervisor has commented on several occasions that the order of subjects should be changed and that some parts should be switched or explained in less/more detail.

Although my supervisor has been incredibly helpful and has provided good pointers, I was wondering if the community here could give some ideas on:

How to keep the structure of a thesis in line and what mistakes to look out for?
Other answers have suggested outlines, but even with such an outline it's not always clear what is the best order to discuss everything (whether it's the choice of section or ordering within a section).

One approach I have seen used is to print out the whole document, cut out each paragraph, and pin them on a pinboard. Then it's easy to adjust the order of the whole document until the whole thing is coherent. You'll probably want to have a pencil on hand while doing this, because you'll need to adjust the text a bit to fit the order.