One thing that needs to be addresses before it gets out of control is making sure that version numbers are embedded into the file name so that we can match definition versions with library versions.

For example the express.d.ts is not for the current version of express.js found at expressjs.com or on Github. The express.d.ts here appears to be for version 2.* of express.

Something like express.2.x.d.ts and jquery.1.8.1.d.ts seems reasonable enough.