I would suggest a drastic change :) No module at all, and no ///reference declaration neither...
I would personnaly prefer :
having to tell the compiler where to find files to compile, eg a config file describing every directories to target (sub-directories will be deduced)... Once done, we don't need to make a ///ref in the code, everything may be find through the config file
2) No module
we don't need modules ; we have classes, and even static declaration for both variables and functions... If you want to modularize, but into stuff classes...
it would be valuable to have a "assembly" statement at the beginning of the file where putting the name of a js. library we want to generate. By default, it would be "app".
So we could generate different .js files from a bunch of ts files, eg collection.js, streams.js, http.js and app.js