Add update-deps skill for automated dependency updates

Defines a Copilot skill that automates the full dependency update
lifecycle for this Rust workspace: discover outdated deps via
dependabot alerts/PRs, apply updates grouped by ecosystem (cargo,
github-actions, npm), fix breakage, get CI green, and create PRs
for human review.

Also adds github/rust-gems to the update-deps-supervisor target list.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

Author: tclem

.github/skills/update-deps/SKILL.md

@@ -0,0 +1,287 @@
+---
+name: update-deps
+description: Keep dependencies up-to-date. Discovers outdated deps via dependabot alerts/PRs, creates one PR per ecosystem, iterates until CI is green, then assigns for review.
+user-invocable: true
+---
+
+# Update Dependencies
+
+Automate the full dependency update lifecycle: discover what's outdated, apply updates grouped by ecosystem, fix breakage, get CI green, and hand off for human review.
+
+## Repository context
+
+This is a Rust workspace containing utility crates published to crates.io. All dependency update PRs target the **`main`** branch.
+
+Dependabot is configured (`.github/dependabot.yaml`) to open PRs against `main` on the 2nd of each month. This skill gathers individual dependabot PRs, combines updates by ecosystem, fixes any breakage, gets CI green, and creates consolidated PRs for human review.
+
+### Crates in this workspace
+
+| Crate | Description |
+|---|---|
+| **bpe** | Fast byte-pair encoding |
+| **bpe-openai** | OpenAI tokenizers built on bpe |
+| **geo_filters** | Probabilistic cardinality estimation |
+| **string-offsets** | UTF-8/UTF-16/Unicode position conversion (with WASM/JS bindings) |
+
+Supporting packages (not published): `bpe-tests`, `bpe-benchmarks`.
+
+### Ecosystems in this repo
+
+| Ecosystem | Directories | Notes |
+|---|---|---|
+| **cargo** | `/` (workspace root) | All Rust deps managed at workspace level via `Cargo.lock` |
+| **github-actions** | `.github/workflows/` | CI and publish workflows |
+| **npm** | `crates/string-offsets/js/` | JS bindings for string-offsets (WASM) |
+
+### Build and validation commands
+
+```bash
+make build     # cargo build --all-targets --all-features
+make build-js  # npm run compile in crates/string-offsets/js
+make lint      # cargo fmt --check + cargo clippy (deny warnings, forbid unwrap_used)
+make test      # cargo test + doc tests
+```
+
+CI runs on `ubuntu-latest` with the `mold` linker. The lint job depends on build.
+
+## Workflow
+
+### 1. Assess repo state
+
+Determine the repo identity and confirm the target branch.
+
+```bash
+git remote get-url origin   # extract owner/repo
+git fetch origin main
+git rev-parse --verify origin/main
+```
+
+Detect which ecosystems have pending updates:
+
+```bash
+[ -f Cargo.toml ] && echo "cargo"
+ls .github/workflows/*.yml .github/workflows/*.yaml 2>/dev/null && echo "github-actions"
+[ -f crates/string-offsets/js/package.json ] && echo "npm"
+```
+
+Report discovered ecosystems to the user.
+
+### 2. Gather dependency intelligence
+
+Fetch open dependabot PRs:
+
+```bash
+gh pr list --author 'app/dependabot' --base main --state open --json number,title,headRefName,labels --limit 100
+```
+
+Fetch open dependabot alerts:
+
+```bash
+gh api /repos/{owner}/{repo}/dependabot/alerts --jq '[.[] | select(.state=="open") | {number: .number, package: .security_vulnerability.package.name, ecosystem: .security_vulnerability.package.ecosystem, severity: .security_advisory.severity, summary: .security_advisory.summary}]'
+```
+
+For ecosystems without dependabot coverage or when running ad-hoc, use native tooling:
+
+- **cargo:** `cargo update --dry-run`
+- **npm:** `cd crates/string-offsets/js && npm outdated --json`
+
+Cross-reference and group all updates by ecosystem. Present a summary to the user:
+
+- How many updates per ecosystem
+- Which have security alerts (and severity)
+- Which dependabot PRs already exist
+
+**Flag high-risk upgrades.** Before proceeding, explicitly call out upgrades that carry elevated risk:
+
+- **Major version bumps** — likely contain breaking API changes
+- **Packages with wide blast radius** — for this repo, pay special attention to: `serde`, `itertools`, `regex-automata`, `wasm-bindgen`, `criterion`, and the Rust toolchain itself
+- **Multiple major bumps in the same PR** — each major bump multiplies the risk; consider splitting them
+
+Present the risk assessment to the user and recommend which upgrades to include vs. defer. When in doubt, prefer a smaller, safe update over an ambitious one that might break.
+
+### 3. Create branch and apply updates
+
+For each selected ecosystem, starting from `main`:
+
+```bash
+git checkout main
+git pull origin main
+git checkout -b deps/{ecosystem}-updates-$(date +%Y-%m-%d)
+```
+
+Apply updates using ecosystem-appropriate tooling:
+
+**cargo:**
+
+```bash
+cargo update
+# For major bumps, edit Cargo.toml version constraints then:
+cargo check
+```
+
+This is a Cargo workspace — always run from the repo root. All crate `Cargo.toml` files are in `crates/`. The `Cargo.lock` at the root is the single source of truth.
+
+**npm:**
+
+```bash
+cd crates/string-offsets/js
+npm update
+npm install
+```
+
+**github-actions:**
+
+- Parse workflow YAML files in `.github/workflows/` for `uses:` directives
+- For each action with an outdated version (from dependabot PRs/alerts), update the SHA or version tag
+- Be careful to preserve comments and formatting
+
+### 4. Build, lint, and test locally
+
+Always run:
+
+```bash
+make lint      # cargo fmt --check + clippy with deny warnings
+make test      # cargo test with backtrace
+make build     # full workspace build (all targets, all features)
+```
+
+If npm dependencies changed:
+
+```bash
+make build-js  # npm compile for string-offsets JS binding
+```
+
+**If the build/lint/test fails:**
+
+1. Read the error output carefully
+2. Analyze what broke — likely API changes, type errors, or deprecation removals
+3. Make the necessary code changes to fix the breakage
+4. Run the pipeline again
+5. Repeat up to 3 times
+
+If still failing after 3 iterations, report the situation to the user and ask for guidance. Do not push broken code.
+
+### 5. Commit and push
+
+Stage all changes and commit with a descriptive message:
+
+```bash
+git add -A
+git commit -m "chore(deps): update {ecosystem} dependencies
+
+Updated packages:
+- package-a: 1.0.0 → 2.0.0
+- package-b: 3.1.0 → 3.2.0
+
+{If code changes were needed:}
+Fixed breaking changes:
+- Updated X API usage for package-a v2
+
+Supersedes: #{dependabot_pr_1}, #{dependabot_pr_2}
+"
+```
+
+Push the branch:
+
+```bash
+git push -u origin HEAD
+```
+
+### 6. Create the PR
+
+**Title:** `chore(deps): update {ecosystem} dependencies`
+
+**Body should include:**
+
+- List of updated dependencies with version changes (old → new)
+- Any security alerts resolved (with severity)
+- **High-risk changes flagged for reviewer attention** (major version bumps, wide-blast-radius packages)
+- Code changes made to fix breakage (if any)
+- References to superseded dependabot PRs
+- Note that this was generated by the update-deps skill
+
+Write the body to a temp file and create the PR **targeting `main`**:
+
+```bash
+gh pr create --title "chore(deps): update {ecosystem} dependencies" --body-file /tmp/deps-pr-body.md --base main
+rm /tmp/deps-pr-body.md
+```
+
+### 7. Monitor CI and iterate on failures
+
+Watch the PR's checks:
+
+```bash
+gh pr checks {pr_number} --watch --fail-fast
+```
+
+**If checks fail:**
+
+1. Get the failed run details:
+
+```bash
+gh run list --branch {branch} --status failure --json databaseId,name --limit 1
+gh run view {run_id} --log-failed
+```
+
+2. Analyze the failure — CI runs on `ubuntu-latest` with `mold` linker, which may differ from local builds.
+
+3. Fix the issue locally, commit, and push:
+
+```bash
+git add -A
+git commit -m "fix: resolve CI failure in {ecosystem} dep update
+
+{Brief description of what failed and why}"
+git push
+```
+
+4. Monitor again. Repeat up to 3 iterations total.
+
+5. If still failing after 3 pushes, report to the user with the failure details and ask for help.
+
+### 8. Close superseded dependabot PRs
+
+For each dependabot PR that this update supersedes:
+
+```bash
+gh pr close {dependabot_pr_number} --comment "Superseded by #{new_pr_number} which includes this update along with other {ecosystem} dependency updates."
+```
+
+### 9. Assign for review
+
+Determine the current user:
+
+```bash
+gh api user --jq '.login'
+```
+
+Request review:
+
+```bash
+gh pr edit {pr_number} --add-reviewer {user_login}
+```
+
+Report the final PR URL and a summary of what was done.
+
+## Guidelines
+
+- **All PRs target `main`.** There is no separate dev branch.
+- **Never push to `main` directly.** Always work on a feature branch.
+- **Never push code that doesn't pass `make lint` and `make test`.** If you can't fix it in 3 tries, stop and ask.
+- **Be conservative with major version bumps.** If a major version update breaks things and the fix isn't obvious, skip that package and note it in the PR description.
+- **Preserve lockfiles.** Always regenerate `Cargo.lock` and `package-lock.json` after updating — don't just edit manifests.
+- **One ecosystem at a time.** Complete the full cycle (update → build → push → PR → CI green) for one ecosystem before moving to the next.
+- **If no updates are needed** for an ecosystem, skip it and tell the user.
+- **Security alerts take priority.** Address security alerts first within each ecosystem.
+- **Clippy is strict.** This repo forbids `unwrap_used` outside tests and denies all warnings. New dependency versions may trigger new clippy lints — fix them.
+
+## Edge cases
+
+- **Cargo workspace:** All Rust dependencies are managed at the workspace root. Always run `cargo update` and `cargo check` from the repo root.
+- **npm is scoped to string-offsets:** The only npm package is in `crates/string-offsets/js/`. Don't look for npm elsewhere.
+- **WASM builds:** After updating `wasm-bindgen` or related deps, verify `make build-js` still works — WASM toolchain version mismatches are common.
+- **Rate limits:** If `gh api` hits rate limits, wait and retry. Report to user if persistent.
+- **Nothing to update:** Report cleanly and move to the next ecosystem (or exit).
+- **Merge conflicts on push:** Rebase on `main` and retry: `git fetch origin main && git rebase origin/main`.
+- **Branch already exists:** If `deps/{ecosystem}-updates-{date}` already exists, append a counter or ask user.