Reorganizing the code
Removed bibliography numbering from ToC
Reorganizing source files...

Divided the main text in various tex files included by using the subfile
package, e.g. "\subfile{introduction}".

Revamped Makefile, so it's possible to generate the PDF by using `make`.

Also created a scripts/ directory for MATLAB (and maybe Ruby/Python)
programs that generate graphics and other figures. It's pretty useful to
have reproducible graphics, as it allows to update them more easily.

Finally, added a imgs/ directory for the finished graphics (or pictures,
etc).