Thesis writing; bottom up vs. top down Situation: I’m completing a master’s degree in computer science. Currently, I’m at the final stage and finishing writing my thesis.

Usually, similar theses in my institute have the following structure:


Introduction.
Literature survey.
Proposed solution, method, framework, ...
Implementation and case studies.
Conclusion.


Problem: Actually, the research problem that I’m undertaking is a little complicated and crosses multiple landscapes; it’s about designing data warehouses using ontology. So the way I have followed is bottom-up, providing a chapter of foundations before the solution chapter (point 3 above). These foundations contain multiple basic definitions, constraints and rules that I build upon in the next chapter (including some novel theoretical issues), in order to give the reader the sufficient tools to launch reading my work.

However, my supervisor told me that this is not the best way, and that reader may be confused with all this much of theoretical knowledge in a bottom up fashion, that may lead to getting lost. Instead, he suggested to define any concept only whenever I need to use it, even if it this concept is proposed by me.

Question: Though I know that there may be no specific answer. However, in such a situation, which is better? bottom up or top down? Any suggestions?
I have not enough reputation to comment. So, we will have to go with an answer. I disagree with Cameron Williams and I agree with your supervisor. Your thesis is not a textbook and front loading in a thesis will not have the intended effect. Frankly, if you start with basically a set of definitions, it is quite likely that your assessors will only cursory read that section. They might then be confused when they read the actual solution chapter because they don't have the necessary understanding of the concepts you thought they would have.

I think you should follow your advisor. Think of your thesis as telling a story where you introduce new concepts at the point where you need them. You can always have a glossary at the end of your thesis to gather all relevant terminology in one place.

The exception to this advice would be if you are writing in an area where there is a lot of confusion around terminology and names of concepts. If your goal is to argue that prior literature was sloppy in naming its concepts and you want to clarify the literature, a discussion of definitions at the start could be warranted.