TypeScript has support for namespaces, and `import` gives you a lot of flexibility. If these aren't sufficient to handle the problem you describe, can you explain how? Can you post a link to the issue you are watching so we can see a better description of the problem you're running into?
Here's a scenario: You write a library that uses Promises, and use bluebird.d.ts for that definition.
For someone to use your library, they will have to download bluebird.d.ts manually and include it. if you (the lib dev) include it yourself, then any other definition of Promise (including if the user has their own bluebird.d.ts definition included) will cause typing collisions.
As someone mentioned, the Typings project might solve this, but there isn't very good communication on this project and the problems it's supposed to solve.