> this https://github.com/phpcr/phpcr.github.com/blob/master/composer.json lets the templates end up in data/templates of my project folder instead of vendor/... - i don't see any value doing that. i installed phpdocumentor through PEAR, if that matters.

That is a known issue at the moment, IIRC it is fixed in the develop version.

> now in the doc file, if i specify the template as relative path, i must run phpdoc as root or get an error about write protection https://github.com/phpcr/phpcr.github.com/blob/master/doc/config/phpdoc.dist.xml (we discussed that at phpbnl i remember)

That is an unfortunate side-effect of the way XSL works; biggest problem is that I have not found a way around this, I intend to take a look at Twigs capability of having multiple search paths but I still need to support XSL :(