Workspace: getActiveProject is dangerously misleading!

[josephjclark]

@doc-han stumbled across a huge issue in the Workspace class.

getActiveProject should really be something like getTrackedProject, because it returns the project.yaml representation of the checked out project, not what's on the filesystem.

Workspace already exposes getCheckedOutProject, which is fine

We need to:

1. Rename the function
2. Check all uses of the function and check whether they should use getCheckedOutProject instead (the checkout CLI stuff certainly does)

[josephjclark]

@doc-han to take over this instead of #1278 (because this is the underlying cause)