I would like to create a github repository with this edited and in a special presentation format. How should I do it? What files the repository should contain and with what contents.
Copyright licenses are based on copyright law. As far as copyright is concerned, a repository isn't a thing and copyright licenses generally don't mention the term 'repository' at all or even a term that is similar.
For copyright purposes, a file is a computer term for how data is organized and which typically holds (part of) a copyrightable work.
Thus, copyright licenses generally have very little requirements about what files are present in a repository. They mainly have requirements about what information is given to the recipients of the work.
For software, there are certain conventions about what files to include in your repository, but those conventions are not universally accepted nor is there a legal reason to follow them.
For non-software works (which the "Git Internals PDF" is and which the CC licenses target) the use of a repository is not a given, nor that a work might consist of multiple files. For that reason, it is sufficient if your repository contains just a single file with the final rendered version of the document, as long as that document contains an attribution of "Git Internals PDF" and is under the CC BY-SA 3.0 license itself. As explained by Creative Commons itself, an ideal attribution contains the title, a link to where the original can be obtained, the author of the original and the license (with a link) under which you obtained the original work.
If you decide to treat your work more like software, with a source code that the final document can be rendered from, that final rendered document should meet the requirements of the CC BY-SA 3.0 license without the need for a separate "license file" because that is the common expectation with literary works.