[Bug] Projects have different output directory structure with same configuration.

<!-- 🚨 STOP 🚨 𝗦𝗧𝗢𝗣 🚨 𝑺𝑻𝑶𝑷 🚨 --> <!-- Half of all issues filed here are duplicates, answered in the FAQ, or not appropriate for the bug tracker. Please help us by doing the following steps before logging an issue: * Search: https://github.com/Microsoft/TypeScript/search?type=Issues * Read the CONTRIBUTING guidelines: https://github.com/Microsoft/TypeScript/blob/master/CONTRIBUTING.md * Read the FAQ: https://github.com/Microsoft/TypeScript/wiki/FAQ --> <!-- If you have a QUESTION: THIS IS NOT A FORUM FOR QUESTIONS. Ask questions at http://stackoverflow.com/questions/tagged/typescript or https://gitter.im/Microsoft/TypeScript --> <!-- If you have a SUGGESTION: Most suggestion reports are duplicates, please search extra hard before logging a new suggestion. See https://github.com/Microsoft/TypeScript-wiki/blob/master/Writing-Good-Design-Proposals.md --> <!-- If you have a BUG: Please fill in the *entire* template below. --> <!-- Please try to reproduce the issue with `typescript@next`. It may have already been fixed. --> **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/ …