typescript - tsconfig - How to set correct compiler output location for multiple directories (Atom) -

suppose have directory structure:

public/     js/         lib/ test/     ts/ lib/     ts/ 

how configure compile lib/ts/*.ts public/js/lib/*.js , test/ts/*.ts public/js/*.js?

i've tried setting separate tsconfig.json in each ts directory desired outdir, add ///<reference file, compiler outputs unwanted directory tree (on save , on build.)

i ended getting wanted layout:

public/     js/         lib/         test/ src/     ts/         lib/         test/ 

in src/ts/test/tsconfig.json:

"outdir": "../../../public/js" 

in src/ts/lib/tsconfig.json:

"outdir": "../../../public/js/lib" 

in src/ts/test/test.ts:

/// <reference path="../lib/coolstuff.ts" /> 

in atom, if you're working in src/ts/lib, building compile files public/js/lib.

if you're working in src/ts/test, build compile *.ts in test - as files referenced. don't see way prevent referenced file compilation, @ least layout go same location.