Allow help folders instead of all pages in the root (jekyll)

[magicDGS]

The help pages can be more organized if the paths are not always on the root (a characteristic from the Jekyll theme that we are using). This will allow to add more features to the current help pages:

• Organize help pages by version. For example, instead of http://magicdgs.github.io/ReadTools, the root for the documentation will be http://magicdgs.github.io/ReadTools/v${current_version}/. In addition, we can re-direct to http://magicdgs.github.io/ReadTools/latest/.
• Host documentation for previous versions (only for mayor/minor, no for patch). That will allow to maintain proper doc history, and allow users to check the docs for previous versions (although unmaintained, and if new errors arraise, they will be point to the latest).
• Avoid name collision in similar pages

This will require to work on the pages and probably move away from the current documentation style. Probably we should start from version 2 onwards...