The Doxygen documentation is available from the OJS documentation page
. The stable release is available here
(this is for OJS 2.4.2; disregard the incorrect version number there) and for the master branch (which will next be released as OJS 3.0a) the documentation is here
We are currently overhauling the way we treat Doxygen documentation; you'll find it's not currently in good shape but we'll be changing that over the coming months.
Public Knowledge Project Team