SWIG files live in their own top-level directory swig.
The wrapper is generated by
swig -tcl -namespace -prefix notmuch -pkgversion 0.1 -I/usr/include notmuch.i
and the resulting file needs to be moved to the generic directory which is where everything else expects to find it.
Note that since notmuch is a library the header file is already on the development system, though swig needs to be told where it is.