Modify doxygen input file to consider all headers

doc/reference.doxygen.in:
Alphabetically sort the list of headers, that doxygen considers.
Add any missing headers.

doc/reference.doxygen.in

@@ -518,18 +518,22 @@ INPUT                  = @top_srcdir@/doc/mainpage.dox \
                          @top_srcdir@/doc/porting.dox \
                          @top_srcdir@/example-clients/inprocess.c \
                          @top_srcdir@/example-clients/simple_client.c \
+                         @top_srcdir@/jack/control.h \
                          @top_srcdir@/jack/intclient.h \
                          @top_srcdir@/jack/jack.h \
+                         @top_srcdir@/jack/jslist.h \
+                         @top_srcdir@/jack/metadata.h \
+                         @top_srcdir@/jack/midiport.h \
                          @top_srcdir@/jack/ringbuffer.h \
+                         @top_srcdir@/jack/session.h \
                          @top_srcdir@/jack/statistics.h \
+                         @top_srcdir@/jack/systemdeps.h \
                          @top_srcdir@/jack/thread.h \
                          @top_srcdir@/jack/transport.h \
                          @top_srcdir@/jack/types.h \
-                         @top_srcdir@/jack/midiport.h \
-                         @top_srcdir@/jack/session.h \
+                         @top_srcdir@/jack/uuid.h \
                          @top_srcdir@/jack/weakjack.h \
-                         @top_srcdir@/jack/control.h \
-                         @top_srcdir@/jack/metadata.h \
+                         @top_srcdir@/jack/weakmacros.h \
 
 # This tag can be used to specify the character encoding of the source files 
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is