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+My web server runs in a chroot jail. This makes things interesting because the paths are slightly different depending on whether you are inside or outside the chroot.
+
+To override an incorrectly guessed path, I set setupconf in the .setup file. I also set allow_symlinks_before_srcdir=>1. However, when I tried websetup, the setup file was correctly changed but these important settings disappeared. This seems like a bug.