[Doc] Enable generation of subdirectories to store the output

The files kinetics.h and onedim.h are present as high-level application 
include files and as lower-level implementation include files. Doxygen 
generates HTML documentation for all files in the same folder, and on 
case-insensitive file systems, the documetation for the application and 
the implementation files will shadow each other. This commit enables the 
option to put documentation files into subfolders in the root directory, 
hopefully separating these "duplicate" files

doc/doxygen/Doxyfile

@@ -50,7 +50,7 @@ OUTPUT_DIRECTORY       = build/docs/doxygen
 # source files, where putting all generated files in the same directory would
 # otherwise cause performance problems for the file system.
 
-CREATE_SUBDIRS         = NO
+CREATE_SUBDIRS         = YES
 
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all
 # documentation generated by doxygen is written. Doxygen will use this