Cookiecutting - modify files v2

[8bitsam]

Fixed version of #45 - modifies files to more closely match the cookiecutter.

[sbillinge]

This looks good, except I don't think examples should be in src as it is not part of the source code, it is rather part of the documentation, no?

We could maybe leave it as is (i.e., the examples stand alone at the top level in an examples dir), or we could slip it under doc so it is doc/examples.

On balance I think I prefer the latter solution.

[8bitsam]

This looks good, except I don't think examples should be in src as it is not part of the source code, it is rather part of the documentation, no?

We could maybe leave it as is (i.e., the examples stand alone at the top level in an examples dir), or we could slip it under doc so it is doc/examples.

On balance I think I prefer the latter solution.

I moved it into doc/.