Doxygen with Windows
Since I move often between Linux, various UNIX flavors, and Windows, I use Cygwin (http://www.cygwin.com/) to provide a sane environment under Windows. Because Doxygen is a Linux-based program, it should be easy to run under Cygwin, right?
In fact, it does work well with Cygwin—but with one caveat. When I first tried running Doxygen, all of the generated graphics in the HTML output were showing up as broken links. Eventually, I realized that the target drive was mounted in Cygwin's text mode, which means that Cygwin was manipulating the line endings in the files. Apparently, Doxygen wasn't opening the images in binary mode, so Cygwin was cheerfully converting them into Windows text format! This, of course, corrupted the files and made them worthless.
The answer is to use a Cygwin file system that is mounted in binary mode. This is the default for the Cygwin mount command (a -t or --text overrides the default). You can explicitly use the -b or --binary flag to the mount command to force binary mode. If you run mount with no arguments, you'll see "(binmode)" after each volume mounted in binary mode.
—A.W.
