#104 Upgrade Rust to 1.99.0 and clean Cargo package exclusions

User description

What / why

Rust pin audit: the repo is already on 1.99.0 everywhere, so no toolchain pin changed. Verified sites:

No .devcontainer/ or .cursor/ directory exists. The only remaining 1.98.1 strings are in committed experiments/usefulness/results/* and REPORT.md, which intentionally record the historical run that produced them (REPORT.md says so explicitly).

Package exclusion cleanup (cargo package --list --allow-dirty): the crate was shipping

• .agents/setup (Cursor Cloud bootstrap script: apt-get + rustup), and
• ~1.9 MiB of experiment result artifacts under experiments/usefulness/results/ (per-run logs, .jsonl.gz traces, summaries).

Both are now in [package] exclude, and REPOSITORY_ONLY in qualify-package.py rejects them so the CI package job fails if they come back. Kept in the package: experiments/usefulness/{PROTOCOL.md,REPORT.md,run.sh,summarize.py,config/,fixtures/} (the usefulness_* examples read those fixtures), .cargo/config.toml (the extracted package needs its libzmq alignment defines; see the comment in qualify-package.py), Cargo.lock (binary crate; --locked is the documented workflow), both licenses, README.md, rust-toolchain.toml.

Package list: 62 files after this change; zero .agents/ or results/ entries.

How verified (Rust 1.99.0, Linux, CPU only)

• cargo fmt --check — clean
• cargo clippy --locked --all-targets -- -D warnings — clean
• cargo test --locked — 159 passed, 1 ignored; config_startup passed
• RUSTDOCFLAGS="-D warnings" cargo doc --locked --no-deps — clean
• CC=gcc CXX=g++ cargo clippy --locked --all-targets --all-features -- -D warnings — clean (libzmq built from source)
• CC=gcc CXX=g++ cargo test --locked --all-features — 182 passed, 1 ignored; config_startup, thalamic_brainstem_smoke, pub_lifecycle passed
• python3 -m py_compile .github/scripts/qualify-package.py — ok (full qualify-package.py not run locally; it needs a clean committed checkout and runs a publish dry-run; the CI package job covers it)

Acceptance checklist

• Every Rust pin site audited and on 1.99.0 (no change needed)
• [package] exclude audited via cargo package --list; agent/CI/devin files and bulky result artifacts excluded; license/README/fixtures included
• Package qualification gate updated to enforce the new exclusions
• fmt, clippy -D warnings, tests (stub + --all-features), rustdoc -D warnings green on 1.99.0
• CI package job (publish dry-run) — runs in GitHub Actions on this PR

Out of scope: publishing, consumer bumps, edition/API changes.

Closes LIM-1514

Generated by Claude Code

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CodeAnt-AI Description

Exclude setup scripts and experiment results from published crates

What Changed

• Published crates no longer include the repository setup script or committed experiment results.
• Package checks now reject those files if they are included again.
• The experiment report links to the results on GitHub instead of expecting them in the crate.

Impact

✅ Smaller crate downloads
✅ No repository setup script in published crates
✅ Experiment results remain accessible on GitHub

@codeant-ai ask: Your question here

@codeant-ai ask: Can you suggest a safer alternative to storing this secret?

@codeant-ai: Your feedback here

@codeant-ai: Do not flag unused imports.

@codeant-ai: review