tsconfig.json fails to save, wrong version returns after server restart

🐛 bug report

Description of the problem

I'm trying to save a tsconfig file with module: "nodenext" under Typescript@next. The UI claims it is saved, but after a server restart or leaving for an hour and coming back, the old version of TSConfig returns claiming I edited it, this usually breaks the sandbox. The zombie files comes back even after deleting the cache and logging back in.

Related to #5598

How has this issue affected you? What are you trying to accomplish?

Hours of lost work debugging phantom zombie files like package.json, .gitignore and tsconfig.json

To Reproduce

1. remove moduleResolution from tsconfig and set module to nodenext.
2. set package.json to typescript@next
3. Have a devDependency

Your Environment

Workaround

Remove devDependencies and peerDependencies if possible, the wreak havoc on CSB sync causing zombie config files to revert. Keep duplicate copies of tsconfig.json, package.json and .gitignore to undo potential damage from CSB's very very broken workdir sync. Also, deleting directories never deletes the workdir directory or any of it's files... this is really unexpected.

A documentation article explaining how CSB's three layer workdir sync process works and why it is so bad would be very helpful. I've resorted to never editing package.json using the UI and instead using vim to modify a backup and overwrite the real version in the container.

Sleuthing

Probably related unusual message:

@CompuIves code in actions.ts, modulePos returns -1 and crashes on the next line

 if (newModule) {
            if (oldModule) {
              const modulePos = oldSandbox.modules.indexOf(oldModule);
              Object.assign(oldSandbox.modules[modulePos], newModule);
            } else {
              oldSandbox.modules.push(newModule);
            }
          }

https://github.com/codesandbox/codesandbox-client/blame/b136899240dd569fbba959a0bcb9e8a9a07f1af2/packages/app/src/app/overmind/namespaces/files/actions.ts#L922

It seemed to be exacerbated by a devDependency after the typescript@next dependency

Reproduce the sync failure with module set to nodenext, typescript@next, and a devDependency. Start in packages/app/src/app/overmind/namespaces/files/actions.ts around line 922, then trace the workdir sync path and the modulePos lookup. Done means saved tsconfig.json and related files remain current after a restart without zombie files returning or the sync action crashing.