Ensure exit codes in more cases

[sophiajt]

Description

This adds more guards to ensure that we've seen an exit code before we move on. There were a few places in the repl and script runner that might have moved on before the external and fully completed. In theory, waiting on the exit code should help.

Tests

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 --all --all-features -- -D warnings -D clippy::unwrap_used -A clippy::needless_collect to check that you're using the standard code style
• cargo build; cargo test --all --all-features to check that all the tests pass