Fixes lingering issues to support workspaces in CLI

[Rexios80]

See #298 (comment)

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[rrousselGit]

Hello there! We'll need tests, as per usual :)

[Rexios80]

I am trying to write a test, but having a hard time getting it to work. This PR is more of a refactor than added functionality. The only code that might be questionable is adding followLinks: false since I thought there was already handling somewhere for that, but I was getting crashes in the ios symlinks folders.

[rrousselGit]

Well if it's fixing something, we need a regression test for it.

[Rexios80]

Do you have any suggestions for where the test should go and other tests I should base it on?

[rrousselGit]

Depends on how you want to implement the test.

I'm not fully understanding the issue that is being fixed here, so I don't know. But you can always write a e2e test and place it next to the other ones (the ones that start a process)