Starting with r39870 the dart2js library files are back in the compiler directory, under `js_lib`.
Normally git (or svn) should do the move transparently and you shouldn't need to worry.
Note that preamble files are in a sub-directory of js_lib, so you might need to update your scripts that run the output of dart2js.
--
Give a man a fire and he's warm for the whole day,
but set fire to him and he's warm for the rest of his life. - Terry Pratchett