Add Joey's patches to the manual (which came from a separate patch).
Move declaration into the .cc file.
Clarify documentation and minor improvements of a line of code.
General update of Joey's first version of the cookbook.

Minor edits to Joey's version.

Edit the text and make the input files so that they get generated by the script and then included into the text, rather than copy-pasted there.

Some renaming and other minor adjustments.

Add an entry.

Comment on depth and height.