Fix overlays not preserving hidden env vars

[kubouch]

Description

Hidden environment variables were reset when you called overlay use on existing environment.

Fixes #6316

Also moves the source-env tests to the command tests.

Tests

Make sure you've done the following:

• Add tests that cover your changes, either in the command examples, the crate/tests folder, or in the /tests folder.
• Try to think about corner cases and various ways how your changes could break. Cover them with tests.
• If adding tests is not possible, please document in the PR body a minimal example with steps on how to reproduce so one can verify your change works.

Make sure you've run and fixed any issues with these commands:

• cargo fmt --all -- --check to check standard code formatting (cargo fmt --all applies these changes)
• cargo clippy --workspace --features=extra -- -D warnings -D clippy::unwrap_used -A clippy::needless_collect to check that you're using the standard code style
• cargo test --workspace --features=extra to check that all the tests pass