misc/doxygen.cfg needs to be updated

misc/doxygen.cfg needs to be updated for the new directory layout. See diff below. Running doxygen misc/doxygen.cfg throws lots of warnings, I'm not sure if this is normal or has to do with changes in the code that have not been reflected in the comments yet.

diff --git a/misc/doxygen.cfg b/misc/doxygen.cfg
index 151c2e1..f13377b 100644
--- a/misc/doxygen.cfg
+++ b/misc/doxygen.cfg
@@ -493,7 +493,7 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories
 # with spaces.

-INPUT                  = src test
+INPUT                  = include src test

 # This tag can be used to specify the character encoding of the source files th
 # doxygen parses. Internally doxygen uses the UTF-8 encoding, which is also the

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