Hi, thanks for reporting !

The misaligned patch is still there in the latest debian packaging:
https://salsa.debian.org/debian/doxygen/blame/master/debian/patches/doxygen-jquery.patch

I have created a bug in debian BTS here: https://bugs.debian.org/943890

Paolo

** Bug watch added: Debian Bug tracker #943890
   https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=943890

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https://bugs.launchpad.net/bugs/1631169

Title:
  doxygen-jquery.patch modification misapplied to dynsection.js

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