Codex created this PR from the following prompt:
> upgrade this entire repo to Rust 1.89. Note that this requires
updating codex-rs/rust-toolchain.toml as well as the workflows in
.github/. Make sure that things are "clippy clean" as this change will
likely uncover new Clippy errors. `just fmt` and `cargo clippy --tests`
are sufficient to check for correctness
Note this modifies a lot of lines because it folds nested `if`
statements using `&&`.
---
[//]: # (BEGIN SAPLING FOOTER)
Stack created with [Sapling](https://sapling-scm.com). Best reviewed
with [ReviewStack](https://reviewstack.dev/openai/codex/pull/2465).
* #2467
* __->__ #2465
This is a small quality-of-life feature, the addition of
`--compute-indices` to the CLI, which, if enabled, will compute and set
the `indices` field for each `FileMatch` returned by `run()`. Note we
only bother to compute `indices` once we have the top N results because
there could be a lot of intermediate "top N" results during the search
that are ultimately discarded.
When set, the indices are included in the JSON output when `--json` is
specified and the matching indices are displayed in bold when `--json`
is not specified.
Update `run()` to take `cancel_flag: Arc<AtomicBool>` that the worker
threads will periodically check to see if it is `true`, exiting early
(and returning empty results) if so.
