Say we have the File structure (--outDir js):

ts
    a.ts
    foo
    |> b.ts
    |> c.ts
js
    a.js
    foo
    |> b.js
    |> c.js

If we compile with all three files with outDir its all okay. But if we only compile b.ts or c.ts with outDir js then we would get a new folder inside ts:

js    
    |> b.js
    |> c.js

Current workaround is to create a .baseDir.ts file under the ts folder and always pass it to the compiler in addition to the individual files.

Workaround from grunt-ts : TypeStrong/grunt-ts#77
Ported from Codeplex : https://typescript.codeplex.com/workitem/2297