## Summary
Add a note in the documentation to clarify that `uv.toml` files take
precedence over `[tool.uv]` section in `pyproject.toml`, based on the
warning shown in the CLI:
```console
$ uv version
warning: Found both a `uv.toml` file and a `[tool.uv]` section in an adjacent `pyproject.toml`. The `[tool.uv]` section will be ignored in favor of the `uv.toml` file.
uv 0.4.2 (Homebrew 2024-09-01)
```
## Summary
Previously, we wouldn't respect configuration files in directories
_above_ a workspace root. But this is somewhat problematic, because any
`pyproject.toml` will define a workspace root...
Instead, I think we should _start_ the search at the workspace root, but
go above it if necessary.
Closes: #5929.
See: https://github.com/astral-sh/uv/pull/4295.
## Summary
This PR deprecates the `--isolated` flag. The treatment varies across
the APIs:
- For non-preview APIs, we warn but treat it as equivalent to
`--no-config`.
- For preview APIs, we warn and ignore it, with two exceptions...
- For `tool run` and `run` specifically, we don't even warn, because we
can't differentiate the command-specific `--isolated` from the global
`--isolated`.
