Sequential addition of optional dependencies [new_extra] of a pypi dependency replaces [previous_extra] instead of appending to the list of extras

[seembha]

Checks

• I have checked that this issue has not already been reported.

• I have confirmed this bug exists on the latest version of pixi, using pixi --version.

Reproducible example

> pixi add pandas[excel] --pypi

adds the following to pixi.toml

[pypi-dependencies]
pandas = { version = ">=2.2.3, <3", extras = ["excel"] }

Now add another [extra]

> pixi add pandas[xml] --pypi

and pixi.toml gets updated to

[pypi-dependencies]
pandas = { version = ">=2.2.3, <3", extras = ["xml"] }

Issue description

This adds support for xml but removes support for excel and is not the expected behavior. The same unexpected behavior is also found for a python project (pyproject.toml).

Expected behavior

The expected behavior should be to append the newly added [extra] to the list of extras

[pypi-dependencies]
pandas = { version = ">=2.2.3, <3", extras = ["excel", "xml"] }

where excel support is preserved and xml support is added.

In short,

> pixi add pandas[excel] --pypi
> pixi add pandas[xml] --pypi

should behave like

> pixi add "pandas[excel, xml]" --pypi

[ruben-arts]

Yes, we should fix this.

Uv behaves similarly, so let's stay close to their design with this.