If you dont have phpdoc installed, you can download the phar version using this or similar. Put the file right in the top directory of tsugi.
curl -O http://www.phpdoc.org/phpDocumentor.phar
On ubuntu you should install:
apt-get install php5-cli
apt-get install graphviz
If you dont install these (i.e. linke on a Mac) you will see this error:
Unable to find the dot command of the GraphViz package. Is GraphViz correctly installed and present in your path?
Run phpdoc as follows
rm -r .tmp_phpdoc .out_phpdoc
php phpDocumentor.phar -c phpdoc.dist.xml
rm -r .tmp_phpdoc
And your documentation will be in .out_phpdoc
The output and parse data have dots by default sothings like grep dont find them by mistake.