Add correct exclusions to Doxyfile.in.

Now that we have src/ext/ext.md (since b0a716dfb0), we
don't want to have src/ext excluded in its entirety.

Like a smart person, when I added src/ext/ext.md, I edited Doxyfile,
forgetting that it is generated from Doxyfile.in.  :/

This should fix travis builds.

Doxyfile.in

@@ -863,7 +863,8 @@ RECURSIVE              = YES
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                = ./src/ext \
+EXCLUDE                = ./src/ext/ed25519 \
+                         ./src/ext/rust \
                          ./src/trunnel \
                          ./src/test \
                          ./src/rust/registry