Converting a lot of *.d.ts files

There are such large projects, written directly in TypeScript and contains complex directory structure with a lot of files (hundreds). Such projects are compiled with option `--declaration` (which autogenerate `*.d.ts` for each `*.ts` files) and [published](https://www.typescriptlang.org/docs/handbook/declaration-files/publishing.html) directly to `npm`
Trying to convert typings of such project, I ran into a number of problems. Here are some of them:

1. Need option to specify directory, from which `dukat` will take `*.d.ts` files recursively and put result to destination directory keeping source directory structure. It could be resolved with some scripting, but...
2. I've tried to specify 200+ `*.d.ts` files via `$ dukat /path/to/**/*.d.ts`. It takes `> 1 hour` to convert them (2-4 files per minute)
3. Option `-b some_package_name` gave no effect. Each file get same package name as it file name. It also don't work for single file. I expect that I can specify same package name for all files. Ability to specify `@file:JsModule("path-to-module")` would be also useful.
4. Interface names like `'T$0'` will be duplicated, because each file converted independently.
5. If one `external class` implement interface from another file, there are no `override` modifier, because each file converted independently.
6. _Notice_: as mentioned [here](https://www.typescriptlang.org/docs/handbook/declaration-files/publishing.html) `package.json` could contain `types` property or `index.d.ts` at the root of the package. It would be nice if also it were ability to analyze dependencies starting from `index.d.ts` before just converting all files from npm package.
Also mainly `index.d.ts` contains re-exports.

No source files or tests are named. Start by tracing the dukat CLI handling of recursive *.d.ts inputs and the -b option, then examine how files are converted independently. Done would require an agreed scope and verification for directory conversion, shared package names, cross-file declarations, and index.d.ts dependency analysis.

Written by the indexing model from the issue text.