Fix rye add and rye remove to create proper tool.rye section on --dev and --exclude flags

[flyaroundme]

Hey!

This is to address issue #1249

Closes #1249

Looks like the [tool.rye] section in pyproject.toml is not created properly if it was not already presented in the file.
This was due to the it not being created as a table.

Tested it like that:

• Have pyproject.toml without [tool.rye] table:

[project]
authors = [{ name = "xxx", email = "xxx@xxx.com" }]
name = "rye-test"
version = "0.1.0"
description = "wasm sample use py2wasm, rust, wasmer, gowasm, wasmedge"
readme = "README.md"
requires-python = ">=3.11.7"


[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

$ rye add --dev ipython

results in
pyproject.toml

[project]
authors = [{ name = "xxx", email = "xxx@xxx.com" }]
name = "rye-test"
version = "0.1.0"
description = "wasm sample use py2wasm, rust, wasmer, gowasm, wasmedge"
readme = "README.md"
requires-python = ">=3.11.7"


[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[tool.rye]
dev-dependencies = [
    "ipython>=8.26.0",
]

Before fix it was:
pyproject.toml

tool = { rye = { dev-dependencies = [
    "ipython>=8.26.0",
] } }
[project]
authors = [{ name = "xxx", email = "xxx@xxx.com" }]
name = "rye-test"
version = "0.1.0"
description = "wasm sample use py2wasm, rust, wasmer, gowasm, wasmedge"
readme = "README.md"
requires-python = ">=3.11.7"


[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[charliermarsh]

Thanks!