Normalize extras in lockfile (#3958)
## Summary
Previously, when we locked something like `flask[dotenv]`, we created
two separate distributions in the lockfile: one for `flask`, which
included the base dependencies, and one for `flask[dotenv]`, which
included the base dependencies _and_ the `dotenv` dependencies. This was
easy to implement, but it meant that we were duplicating all of the
distribution files for every extra, and duplicating all of the base
dependencies for every extra.
This PR normalizes the data such that we now have one entry per
distribution (i.e., `ExtraName` was removed from `DistributionId`), with
an optional dependencies table with an entry per extra, like:
```toml
[[distribution]]
name = "project"
version = "0.1.0"
source = "editable+file://[TEMP_DIR]/"
sdist = { url = "file://[TEMP_DIR]/" }
[[distribution.dependencies]]
name = "anyio"
version = "3.7.0"
source = "registry+https://pypi.org/simple"
[distribution.optional-dependencies]
[[distribution.optional-dependencies.test]]
name = "iniconfig"
version = "2.0.0"
source = "registry+https://pypi.org/simple"
```
This requires a bit more work upfront, because we now need to merge
multiple packages from the `PetGraph` representation when creating the
lockfile.
Closes https://github.com/astral-sh/uv/issues/3916.
