Maintain src/ folder structure when building to dist/ folder with Typescript 3
I had a similar problem when initially converting to a Typescript project. I also set resolveJsonModule: true and the src directory was copied to the output dist directory.
The underlying reason is that one of my source files required package.json at the root of the project. Once i removed that, tsc no longer added src to the dist directory.
In short, make sure you are not requiring files outside of your src directory.
Explanatory FAQ here: https://github.com/Microsoft/TypeScript/wiki/FAQ#why-does---outdir-moves-output-after-adding-a-new-file
The upgrade from TypeScript 2 to 3 by itself shouldn't have changed the behavior; if we can confirm that it did, that may be a bug. In any case, check that the rootDir compiler option points to your src directory and not to the parent directory, because the structure under the rootDir is what is mirrored under the outDir.
The structure of the output directory is controlled by the rootDir of the compilerOptions. See documentation here, setting it to ./src should solve the issue.
{ "compilerOptions": { "rootDir": "src", ... }, "include": [ "src/" ]}