Review: needs rebase after #1283

PR #1283 (setup phase split) has been merged. This PR overlaps with it on with_options.rs, causing merge conflicts.

Action needed: Please rebase onto main and remove the with_options.rs changes (they're now superseded by #1283). Only the pack-specific changes (pack/create_args.rs, pack/mod.rs) should remain.

Alternatively, I can close this PR and you can re-submit with just the pack refactoring scope.

Integrated via cherry-pick and rebase onto main (commit f433a58d8 → rebased as 6c14ad18d).

Applied the guard-clause refactoring for maybe_add_project_root_warning, maybe_spawn_background_index, and maybe_enable_ide_config_access. Merge conflict with #1283 resolved manually.

Quality gate passed: cargo fmt --check + cargo clippy --all-features -- -D warnings.

Thank you @cedric013 for the contribution!

Refs #1277