generated-site no longer working

the changes to find document files at the start means that generated-site, coming from reports, don't exist and are thus never rendered. We could reprocess this directory last, but this isn't optimal.

Ultimately, want to get rid of generated-site in favour of reports, but some reports use it to generate multiple pages which the api doesn't support unless it is straight to html and outside doxia, or to pipeline through formats (something -> xdoc -> html).