Repository: TypeScript
Issue: [Bug] Projects have different output directory structure with same configuration.
Labels: Needs Investigation

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**TypeScript Version:**  4.0 (npm)

<!-- Search terms you tried before logging this (so others can find this issue more easily) -->
**Search Terms:** 
declarationDir, rootDir, baseURL.

**Problem**
My app has a circular reference between the client and the server for typing reasons, essentially during prototyping there is a proxy that allows the server and the client to call functions on the remote as though they were local asynchronous functions. This has traditionally worked *fine* (well, with effort) but lately my server tsconfig seems to want to output files in a different directory structure than it was previously, without warning (I didn't change the tsconfig file). Here's what's happening:

**Expected behavior:**
The folder structure should look like this:
```
Project:
    Client/
        tsconfig.json <--"Client tsconfig"
        code.ts
        code.js
    ClientDeclarations/
        code.d.ts
    Common/
        code.ts
        code.d.ts
        code.js
    Server/
        tsconfig.json <-- "Server tsconfig"
        code.ts
        code.js
    ServerDeclarations/
        code.d.ts <-- ! Note server files are meant to be at the root of the output dir
    tsconfig.json <-- "Parent tsconfig"
```

**Actual behavior:**
Instead it looks like this:
```
Project:
    Client/
        tsconfig.json <--"Client tsconfig"
        code.ts
        code.js
    ClientDeclarations/
        code.d.ts
    Common/
        code.ts
        code.d.ts
        code.js
    Server/
        tsconfig.json <-- "Server tsconfig"
        code.ts
        code.js
    ServerDeclarations/
        Client/
             code.d.ts <-- ! This is the client's .d.ts files which shouldn't be output by the server tsproj!
        Server/
             code.d.ts
    tsconfig.json <-- "Parent tsconfig"
```

**Code**
This is the "Parent tsconfig" (note I am using ttypescript):
```ts
{
  "compileOnSave": false,
  "compilerOptions": {
    "target": "es6",
    "sourceMap": true,
    "strict": true,
    "plugins": [
      { "transform": "../Typescript/SuperTransform.js" },
      { "transform": "../Typescript/Macros.js" }
    ]
  },
  "exclude": [
    "node_modules"
  ]
}
```

This is the client config (I don't think the references section is used on the client, it's just there to keep the client and server configs similar):
```ts
{
  "compileOnSave": false,
  "extends": "../tsconfig.json",
  "compilerOptions": {
    "module": "amd",
    "target": "es6",
    "lib": [ "es6", "dom" ],
    "sourceMap": true,
    "strict": true,
    "build": true,
    "declaration": true,
    "declarationDir": "../ClientDeclarations",
    "baseUrl": "./",
    "paths": {
      "@Common/*": [ "../Common/*" ],
      "@Server/*": [ "../ServerDeclarations/*" ],
      "@Client/*": [ "./*" ]
    }
  },
  "include": [
    "./*",
    "./External/koco.ts",
    "./External/kocss.ts",
    "./External/kopath.ts"
  ],
  "exclude": [
    "node_modules"
  ],
  "references": [
    { "path": "../Common" }
  ]
}

```

This is the server config (on the server I'm using module-alias):
```ts
{
  "compileOnSave": false,
  "extends": "../tsconfig.json",
  "compilerOptions": {
    "module": "commonjs",
    "target": "es6",
    "lib": [ "es6", "dom" ],
    "sourceMap": true,
    "strict": true,
    "build": true,
    "declaration": true,
    "declarationDir": "../ServerDeclarations",
    "baseUrl": "./",
    "paths": {
      "@Common/*": [ "../Common/*" ],
      "@Client/*": [ "../ClientDeclarations/*" ],
      "@Server/*": [ "./*" ]
    }
  },
  "include": [
    "./*"
  ],
  "exclude": [
    "node_modules",
  ],
  "references": [
    { "path": "../Common" }
  ]
}
```
Note that the only difference between the client and the server is that they have a different module output type and the client includes a few more files.

I've tried adding "../Client" and "../Client/**" to the list of excludes on the server tsconfig but that didn't do anything. I also tried adding rootDir to be the same as baseUrl but that also didn't do anything. Interestingly removing baseUrl and adding rootDir had the desired effect (although is not usable because I need to use paths).

**Playground link**
This issue cannot be reproduced on the playground.

**Related Issues:**
I could not find any related issues.