Use environment layering for `uv run --with` (#3447)
## Summary
This PR takes a different approach to `--with` for `uv run`. Now,
instead of merging the requirements and re-resolving, we have two
phases: (1) sync the workspace requirements to the workspace
environment; then (2) sync the ephemeral `--with` requirements to an
ephemeral environment. The two environments are then layered by setting
the `PATH` and `PYTHONPATH` variables appropriately.
I think this approach simplifies a few things:
1. Once we have a lockfile, the semantics are much clearer, and we can
actually reuse it for the workspace. If we had to add arbitrary
dependencies via `--with`, then it's not really clear how the lockfile
would/should behave.
2. Caching becomes simpler, because we can just cache the ephemeral
environment based on the requirements.
The current version of this PR loses a few behaviors though that I need
to restore:
- `--python` support -- but I'm not yet sure how this is supposed to
behave within projects? It's also left unclear in `uv sync` and `uv
lock`.
- The "reuse the workspace environment if it already satisfies the
ephemeral requirements" behavior.
Closes #3411.
