Ok, so i'll start by saying again there is indeed no really good way to do this with webpack, and unless this is an enormous project, moving to external modules is the way to go.
if most of your files look like this:
//a.ts
module a.b.c {
export class A {}
}
//b.ts
module d.e.f {
export class B extends a.b.c.A
}
Than it's relatively easier, you just do:
//a.ts
export module a.b.c {
export class A {}
}
//b.ts
import {a} from './a';
module d.e.f {
export class B extends a.b.c.A
}
However, in the example you gave, you have two files composing the same namespace\internal module - a.b.c
. This is harder to deal with and you'll need to do some ugly stuff like:
//b.ts
import {aImported} from './a';
module a.b.c {
export class B extends aImported.b.c.A
}
In this solution, your files are external modules and they export internal modules.
There is also a different approach, which is to take all your old code, and compile + concat it old school using Gulp\Grunt, before passing the resulting js file to webpack. I did this in the past and I regret it and has since moved away from it. But it does require the least amount of changes to code which is the main benefit of it. Overall, I think it's even worse than the previous solution...