Thanks, can you help me with the syntax there, I had

exe myname
    : myname.cpp
    : <include>.
    :<include>/usr/local/include/boost-1_39/
    ;

in my Jamroot file. Putting just

<include>/usr/local/include/boost-1_39/

(with or without a trailing semicolon) just below my 'darwin ;' entry  in user-config.jam does not work.

Thanks,

Markus