fix(prune): copy pnpm workspace file to top level out directory (#5605)
### Description
Fixes #5599
In the Go code we put the workspace spec file in `out` instead of
`out/json` where it should be as it is required for install. This means
that many users have a `COPY out/pnpm-workspace.yaml .` line in their
`Dockerfile`s and the removal of the top level copy resulted in a
breakage.
### Testing Instructions
Added integration test to verify contents of the top level `out`
directory.
Co-authored-by: Chris Olszewski <Chris Olszewski>