To build and install the the cocoa# bridge you need to run
./autogen.sh
make

to see monodoc you need to do the following:
cd monodoc
cp Makefile.am Makefile
make


to see tests you need to do the following
cd test
cp Makefile.am Makefile
make

Note, that these are temporary workarounds until autoconf is updated to work with these again.

run and run2 are special targets that will build and run CocoaSharpBrowser.app 
and CocoaSharpFinder.app
make run
make run2
