Preface and notes

I have set it up as a template for the Master thesis on the meta analysis of the interventions that are based on Internet to mitigate longer term smoking cessation.

The way to use this:

Double click anywhere on the text chunk and start editing it.
You can use a large BibTex database for your citation management.
Use simple markdown format to write your paper
You can use bold (B), italics (I), write codes (<>), bullet points, numbered lists, quotes, use hyperlinks and three levels of headings.
Tables can either be inserted as LaTeX tables (which you may not know how to), or as figures. You can insert figures by clicking figure from the space below the chunk and insert the figure (or table as figure)
As much as possible, use the text to write your thesis, Please do not change the layout.md file at all.
Write in plain text, and use markdown syntaxes when you write in your own software. Plenty of software other than word will allow you for this sort of writing. Even notepad or onenote will allow you to write in simple text.
Produce all your tables as csv files and we can change from one format to anotehr. You can then copy and paste your files from a spreadsheet format to the webpage. There are several tools here:

All your figures can be in a separate section and then immediately after the figures, you can insert captions and headers. That way everything remains neat. If you want, you can also embed figures within text by using the markdown formats for figures but I'd rather avoid that in a long document.

Advantages

You can see the entire thesis and paper on one page
We can work simultaneously in the different sections
Comments can be made aside
It has version control system so nothing can be lost
It is easy and time saving
Very very simple to work with
All formatting are correctly done and done at the end of writing this
Very flat learning curve
References are managed automatically (if you are not sure, I shall show you how)

Possible Discomforts

You may not have used anything like this before
The interface may be unfamiliar
Need to work on the browser