Changes how the CLI generates and manages Lima VM configs to make
changes like mounted directories be accurately reflected in Lima.

trellis-cli used to generate a config for Lima in
`.trellis/lima/{name}.yml` which was used for the initial creation of
the VM. However, even when providing a config to `limactl create`, Lima
creates a separate config in its managed directory (`$HOME/.lima/{name}/lima.yaml`).

This meant that any subsequent config changes in Trellis might only be
persisted to the CLI's managed config (in `.trellis`), which would do
nothing, instead of Lima's config.

For example, if you added a new site to Trellis (or changed the path to
an existing one), you'd either have to delete the VM entirely and start
over, or manually make the changes to Lima's config.

This PR removes the old CLI managed config entirely and instead updates
Lima's config directly (the one in `$HOME/.lima`). This means one less
file to manage and a single source of truth which will allow proper VM
udpates.

Now if you change any wordpress sites in development, stopping and
restarting the VM will apply the new config changes.