Frossie is out of the office so I'm assigning this ticket to myself. I'm still unsure of why the doxygen behavior has changed – I'm going to try to the doc build in a clean sandbox env to rule out any persistent state issues.

To reproduce the problem:

• download the lsstDoxygen package
• cd lsstDoxygen
• setup -r .
• scons
• # choose a package for which to generate docs. It takes a long time to generate docs for lsst_distrib whereas afw is fast and shows the problem, so I recommend afw, but meas_algorithms is another good choice
• setup afw
• makeDocs afw

The problem may be in how makeDocs processes the INPUT line of the package's doxygen config is handled. For the afw package I observe that the INPUT line contains several paths (each path is surrounded by double quotes separated from the next by spaces), but the code tries to process all of them as one. As a consequence the code never looks for the main page in the doc directory, but instead only looks in the src directory (the path to src is the last entry on the INPUT line). If so, one fix is to split the INPUT line and process each path separately. Another is to write multiple INPUT lines, one per path (if Doxygen supports that). Splitting the line will take a bit of work, since the code should support spaces within the paths. It also raises the question of how this code ever worked (perhaps the config files used to have multiple INPUT lines?).

Frossie Economou worked out that it was one of my fixes for sconsUtils to work on El Capitan in DM-3200 that broke the doxygen build. It seems that lsstDoxygen makeDocs does not understand that doxygen.conf can use quoting to separate entries (the quoting was needed to deal with paths containing spaces and that was needed on my El Cap test system). I have reverted the sconsUtils patch that did this and I will do a proper fix in another ticket. Frossie Economou tested this branch with buildbot and it did fix the problem.