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It will be common scenario where you want to store your classes and interfaces in separate ts files. It will also be expected that your app's .js file should be able to reference all these compiled versions. Instead of adding all the js files to your html pages, you can compile multiple ts files down into a single js file.
If you app is very simple, you can do this by compiling all of your ts files into a single js file.
file1.ts, file2.ts, file3.ts ==>> app.js
This can be done with a single "root" tsconfig.json file.
That said, your app may be more complicated and require several compiled js files through-out your app. You can do this by having a "base" config file and then a specialized config file in any given subdirectory. The will inherit all of the settings defined in the base config file and then apply it's own overrides.
// patterns:
// . - current directory
// ** - look thru all sub directories
// *.ts or *.* all valid ts extensions
"include": [
"./**/*.*"
]
http://www.typescriptlang.org/docs/handbook/tsconfig-json.html