I suddenly realised the issue with "cocoon-trunk". It needs to run its 'build docs' before running 'forrest'. It generates some extra source documentation before forrest starts.
There is a global parameter "forrest-exec" which can call a shell script to do other things, then call forrest. I have the forrestbot working now for cocoon-trunk. There is potential to have multiple cocoon-trunk builds running, so i am currently finding a way to avoid that. --David