chore: Push FileManager population up to nargo_cli

[kevaundray]

Description

This tries to undo some of the changes done in #3496 where cli methods were moved into the nargo library. This pushes the populating of the file manager up to the cli commands, in most places this is just after the workspace has been resolved.

A possible next step after this is to have the nargo library to no longer ask for a file manager struct, but instead it asks for a FileManager trait which the previous FileManager struct would implement.

Problem*

Resolves

Summary*

Additional Context

Documentation*

Check one:

• No documentation needed.
• Documentation included in this PR.
• [Exceptional Case] Documentation to be submitted in a separate PR.

PR Checklist*

• I have tested the changes locally.
• I have formatted the changes with Prettier and/or cargo fmt on default settings.

[kevaundray]

This does not entirely push population of the FileManager to the cli because noirc_driver adds the stdlib content to the file manager

[TomAFrench]

Let's use the explicit workspace root rather than relying on relative paths.

[TomAFrench]

LGTM