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Compiler outputs files to the wrong directory structure #5809

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@enlight

Description

@enlight

I've noticed a couple of issues with the way the compiler resolves the output directory structure. I've created a minimal project that can be used to reproduce these issues, it's setup as an NPM package, so after cloning/extracting run npm install to install the latest nightly build of TypeScript (support for filenames in the --project compiler option was added very recently).

Issue 1

From the package root run

node ./node_modules/typescript/bin/tsc --project src/good-tsconfig.json

Note that the output directory structure is (as expected):

lib/
  first/
    file1.js
  second/
    file2.js

Now run

node ./node_modules/typescript/bin/tsc --project src/bad-tsconfig.json

Note that the output directory structure is missing the subdir second:

lib2/
  file2.js

While the expected output directory structure is:

lib2/
  second/
    file2.js

Issue 2

I'm not sure if this is a bug or just user error, but it can be reproduced starting with TypeScript 1.6.2 (and possibly earlier, that's just the oldest version I've tried). Run

node ./node_modules/typescript/bin/tsc --project src/second

Note that the output directory structure is:

lib3/
  second/
    first/
      file1.js
    second/
      file2.js

While the expected output directory structure is:

lib3/
  first/
    file1.js
  second/
    file2.js

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