Removed some comments and some Ipsum Lorem
Added part about Reproducible Research
Added more indeces to the introduction. Added a reference for Reproducible Research.
Fixed hyperrefs in index.
Added rubber as a dependency. Use rubber for the build and adapt clean.
Added index terms. Removed Latin example text. Removed log file. Removed Template Chapters.
Added some minimal text to all sections in chapter 1
Added minimal text paragraphs for the sections in Chapter 2.
Added minimal sections for Chapter 3.
Add minimal section paragraphs in Chapter 4.