update-deps

Superpowered Dependabot. Auto-discover all outdated packages, preview them grouped by severity so you can snooze any you are not ready for, audit overrides, apply codebase migrations for major bumps, resolve dependency conflicts, and run the quality gate. In CI it runs unattended (no preview); interactively it shows the preview first. On a main/master run it opens the PR and merges it once checks are green, then cleans up locally; on any other branch it pushes and leaves the PR to you.

Pre-flight: Worktree check

This wrapper writes a new pnpm-lock.yaml and opens a PR, both belong on the main checkout, not a per-SPEC worktree branch. If invoked from a linked worktree, reject hard with a message that surfaces the cached state from main so the user knows whether action is even pending.

Detection (run this first, before anything else):

. .gaia/scripts/main-only-lib.sh
gaia_update_deps_state_line() {
  local cache_file="$1"
  [ -f "$cache_file" ] && command -v jq >/dev/null 2>&1 || return 0
  local outdated_count checked_at
  outdated_count="$(jq -r '.outdatedCount // 0' "$cache_file" 2>/dev/null)"
  checked_at="$(jq -r '.checkedAt // 0' "$cache_file" 2>/dev/null)"
  [ -n "$outdated_count" ] && [ -n "$checked_at" ] && [ "$checked_at" != "0" ] || return 0
  local now age ago_unit ago_value
  now=$(date +%s)
  age=$((now - checked_at))
  # Format age as <Nm ago> / <Nh ago> / <Nd ago>.
  ago_unit="s"; ago_value="$age"
  if [ "$age" -ge 86400 ]; then ago_unit="d"; ago_value=$((age / 86400));
  elif [ "$age" -ge 3600 ]; then ago_unit="h"; ago_value=$((age / 3600));
  elif [ "$age" -ge 60 ]; then ago_unit="m"; ago_value=$((age / 60));
  fi
  printf 'Cached on main: %s packages outdated (last checked %s%s ago).\n' "$outdated_count" "$ago_value" "$ago_unit"
}
gaia_refuse_if_worktree "/update-deps" gaia_update_deps_state_line || exit 1

If the detection does not fire, fall through to the existing ## Pre-flight: Branch check section.

Pre-flight: Branch check

git branch --show-current

If the current branch is main or master and not running in CI, set a flag (SHOULD_CREATE_BRANCH=true) but do not create the branch yet, branch creation is deferred until after Phase 1 confirms there are packages to update. Creating a branch when there is nothing to update pollutes the branch list.

In CI (CI=true, set by GitHub Actions, GitLab CI, CircleCI, and most CI providers), skip branch creation, the workflow owns branch management and pre-creates the appropriate branch before this skill runs.

Otherwise set SHOULD_CREATE_BRANCH=false and proceed on the current branch.

Composition: --scope <group-name>

When invoked with --scope <group-name> (e.g. /update-deps --scope react-router):

• Skip Phase 0 (override audit), out of scope for a single-group run.
• Skip the discovery + preview phase, no preview runs in --scope; the group's members are known from the companion-group table.
• Skip wave classification, the run is implicitly a single group; treat it as Wave A if all members are minor/patch, else Wave B.
• Wave A / Wave B still apply, scoped to the named group's members in root package.json.
• Quality gate, return value, and final report still run.

Used by the GAIA CI update-deps workflow's wave-B matrix shards to fan out one PR per major-bump group.

Companion groups (reference)

The fixed table mapping each package to its group. gaia update-deps run resolves grouping internally and is the source of truth at runtime; every emitted entry already carries its resolved group. When any member of a group is outdated, all members present in package.json update together, so a group moves as one unit (and snoozes as one unit).

Packages not matched form singleton groups. typescript is deliberately one of them: a compiler bump and an ambient type-definition bump (@types/node) carry independent risk and independent migration guides, so they never move as a unit.

Phase 1: Discover, preview, decide (orchestrator)

Discover deterministically via the CLI primitive, the single source of truth for grouping, the ESLint 9.x cap, the gaia.updateDepsHold config hold, and the release-age cooldown (all already applied):

updates_json="$(mktemp)"
.gaia/cli/gaia update-deps run --emit-updates "$updates_json"

Read the payload. If total_count is 0, print All packages are up to date. and exit (no branch, no changes). Each wave_a[] and wave_b[].packages[] entry carries bucket (patch | minor | major | nonsemver), current, latest, group, is_pinned, and kind. total_count is the genuine-upgrade count; actionable_count is for the statusline only (it already subtracts local snoozes), ignore it here.

snoozed[] lists the groups the human deferred earlier that still match the currently-offered targets. Each entry carries group, targets, snoozed_at, and resurfaces_at (ISO stamp when the snooze lapses). Build snoozedGroups, the set of their group ids, this is what you mark and default-skip below. It is empty in CI and whenever no active snooze matches the current offer.

skipped[] entries with reason: "held" are packages capped by the committed gaia.updateDepsHold map in package.json (a durable version ceiling, distinct from a snooze: it holds in CI too and never lapses until the maintainer lifts it). They are already excluded from both waves, never installed, so nothing to apply. Surface them once (see Preview) so the maintainer remembers a hold is active.

A hold caps only the package it names; a coupled sibling in the same companion group (e.g. @vitejs/plugin-react beside a held vite) still updates on its own line. If a sibling release's peer range demands a version above the ceiling, hold the sibling too by adding it to the map. The quality gate catches a peer conflict before merge regardless.

In CI (CI=true) or with --scope <group>, skip the preview and decision entirely. The apply set is the full payload (CI) or the named group (--scope); jump straight to the apply phases with an empty skip set and no ledger write.

Preview

Group the entries for display into four sections in this order: Major, Non-semver, Minor, Patch. A companion group (any group not prefixed singleton:) renders as ONE block under the section of its most-severe member (severity major > nonsemver > minor > patch) and is a single choice that updates together. Render each row as name current → next; for a companion group, list its members under one labelled block (e.g. "react-router group, updates together").

Mark every group in snoozedGroups with a trailing [snoozed until <date>] (the entry's resurfaces_at, rendered as a plain date). Snoozed groups are default-skipped: they are excluded from the default apply set, so a group the human already deferred is not silently re-applied each run. The human can still choose to refresh them.

If skipped[] has any reason: "held" entries, print one line above the sections listing them, e.g. Held by config (not offered): vite (current 8.0.16, ceiling 8.0). This is informational, held packages are never part of any apply set; the line just keeps the active holds visible.

If update_deps.mode in .gaia/automation.json is ci, first print one line: CI owns updates; snoozing here only quiets your local statusline.

Then ask with AskUserQuestion (single-select). When snoozedGroups is non-empty, offer these options in this order:

• Update the rest (default, first option): apply every group EXCEPT the snoozed ones; leave the snoozes intact.
• Choose what to skip: the human names further package or group names to skip; the snoozed groups stay skipped too.
• Update everything incl. snoozed: apply every group AND clear the snoozes.
• Cancel: exit now, no branch, no changes, no ledger write.

When snoozedGroups is empty, offer the original three:

• Update all (default, first option): apply every group.
• Choose what to skip: the human names the package or group names to skip; everything else applies.
• Cancel: exit now, no branch, no changes, no ledger write.

Decision

The skip set is snoozedGroups plus whatever the human names; the apply set is every remaining group. The ledger is full-replace, so any decline --skip call must name every group that should stay snoozed (the pre-existing snoozes AND any newly named), or the omitted ones are dropped from the ledger.

• Update the rest (snoozed groups present) → apply set = payload minus snoozedGroups. Leave the ledger untouched (the snoozes already match the current targets), no decline call. If the apply set is empty (every outstanding group is snoozed), print Snoozed N group(s); nothing else to update. and exit (no branch).
• Update all (no snoozed groups) → clear any prior snoozes, apply everything:

  .gaia/cli/gaia update-deps decline --clear
  

  Apply set = the full payload.
• Update everything incl. snoozed → same action as Update all: clear the snoozes (decline --clear) and apply the full payload.
• Choose what to skip → collect the names, union with snoozedGroups, then record the whole skip set:

  .gaia/cli/gaia update-deps decline --source "$updates_json" --skip "<snoozed…,named…>"
  

  Each name expands to its whole companion group (a partial group cannot be skipped); an unknown name errors so you can re-ask. Apply set = the payload minus the skip set. Echo the resulting apply set back for confirmation. If the apply set is now empty (everything is skipped), print Snoozed N group(s); nothing else to update. and exit (no branch).
• Cancel → stop here.

The snooze ledger (.gaia/local/declined-updates.json) is local-only and gitignored: it suppresses the statusline nudge and default-skips the group in this preview until a newer version ships or 14 days pass. It never HARD-gates a run, the human can always choose to refresh a snoozed group, and CI ignores it entirely (CI is the freshness backstop and keeps opening PRs).

Carry the apply set (filtered wave_a and wave_b) into the phases below.

Override audit + Wave A: Haiku agent

Spawn a Haiku agent (model: "haiku") to run the override audit and the Wave A batch install on the apply set computed above. Pass it these instructions verbatim, substituting the apply set's Wave A entries into the Wave A input:

Phase 0: Override audit

Each key in the top-level overrides: map in pnpm-workspace.yaml exists for one of two reasons: to resolve a peer-dependency conflict, or to enforce a security floor (pin a transitive dependency at or above a patched version to clear a known advisory). The two are detected by different tests, and an override is obsolete only when removing it regresses neither. A peer-dep test alone is blind to security-floor pins (a CVE pin never produces a peer-dep error), so it would wrongly delete every one of them. (pnpm 11 reads overrides here; the package.json pnpm.overrides field is no longer honored.)

Capture the advisory baseline first, with every override still in place:

pnpm audit --json 2>/dev/null | jq -r '.advisories // {} | keys[]?' | sort -u > /tmp/audit-baseline.txt

Each .advisories key is one advisory ID; this file is the set of advisories the current overrides tolerate. (If a future pnpm emits the vulnerabilities shape instead of advisories, read whichever key is present, the goal is a stable ID set to diff against.)

Then, for each override key, one at a time, leaving every other pnpm-workspace.yaml setting untouched:

1. Temporarily remove that single key from the overrides: map.

2. Run pnpm dedupe. A bare pnpm install, even pnpm install --force, short-circuits with "Already up to date" when only the overrides: map changed and leaves the lockfile untouched, so the toggle would not re-resolve and the test below would read the stale tree; pnpm dedupe performs a full install that re-resolves and applies the override change. See wiki/dependencies/pnpm-overrides.md. If it exits non-zero, restore the key, note as retained (install error), and move to the next key, do not diagnose the failure or run the tests below for this key.

3. Peer-dep test: run pnpm ls 2>&1 and scan for peer-dep errors.

4. Security-floor test: run pnpm audit --json and extract its advisory IDs the same way. Any ID present now but absent from /tmp/audit-baseline.txt means removing this override reintroduced a known vulnerability.

   pnpm audit --json 2>/dev/null | jq -r '.advisories // {} | keys[]?' | sort -u > /tmp/audit-now.txt
   comm -13 /tmp/audit-baseline.txt /tmp/audit-now.txt   # IDs this removal introduced
   

5. Decide:

   • Peer-dep errors or any newly introduced advisory → the override is load-bearing. Restore the key. Note as retained (record which test failed, and the advisory ID + package if it was the security-floor test).
   • Neither regressed → the override is obsolete. Leave it removed. Note as removed.

The security-floor test is severity-agnostic on purpose: an override is a deliberate maintainer artifact, so any advisory it was silencing, at any severity, is reason to keep it. This is intentionally stricter than the high/critical surfacing floor in .claude/rules/dep-audit.md: deciding whether to delete a maintainer's pin warrants more caution than deciding whether to surface an advisory for review. A maintainer who wants a pin gone removes it by hand.

After the toggle loop, assert the lockfile matches config. Once every retained key is restored, the lockfile's top-level overrides: block must list exactly the keys present in the overrides: map in pnpm-workspace.yaml. Compare the two; on any drift (a config key missing from the lockfile block, or vice versa) the floor is unapplied, so run pnpm dedupe once more and re-run the quality gate. This assertion is the guarantee that the audit never leaves a stale, silently-disabled security floor. Note the tradeoff: pnpm dedupe re-optimizes the whole tree, so a single toggle can yield a wider lockfile diff than the one key it touched (it may also drop now-redundant transitives). That broader diff is expected, and correct, the alternative is an unapplied override.

Wave A input

You are given the Wave A apply set: the wave_a entries from the orchestrator's discovery, minus any group the human chose to skip. Each entry carries name, current, latest, is_pinned, and kind (minor or patch). Do not run pnpm outdated or re-discover, the ESLint 9.x cap, the release-age cooldown, and companion-group expansion are already applied. If the Wave A apply set is empty, skip straight to the quality gate (Wave B groups, if any, are handled by the orchestrator).

Wave A (batch minor/patch)

1. Build install args. For each entry: if is_pinned use the exact target, else use ^<latest>. Example: pnpm add [email protected] bar@^4.5.0 ....
2. Run the single pnpm add command.
3. Run pnpm ls 2>&1. Scan for peer-dep errors.
4. On error: try one targeted fix in the overrides: map in pnpm-workspace.yaml (e.g. add a parent>child pin), then pnpm dedupe to apply it, a bare pnpm install won't re-resolve an overrides-only change.
5. If still failing: revert the offending packages (pnpm add <pkg>@<previous>) and log them as skipped with the reason.
6. Run the quality gate (below). If it fails, revert the entire Wave A batch.

Quality gate

pnpm typecheck
pnpm lint
pnpm test --run
pnpm pw
pnpm build

Return value

Report back to the orchestrator with:

• Override audit results (removed / retained)
• Wave A results (updated packages, any skipped)
• Quality gate results

Branch creation (after discovery)

Phase 1 already exited if nothing was outstanding or the human cancelled or skipped everything, so reaching here means the apply set is non-empty. After the Haiku agent returns:

• Updates were confirmed. Immediately bust the update-check cache so the statusline reflects the post-update state on the next session regardless of whether this run completes. Use the Write tool to overwrite .gaia/local/cache/shared/update-check.json, preserving gaiaCurrent, gaiaLatest, gaiaHasUpdate, and serenaLangDrift from the existing cache (read it first), but setting outdatedCount to 0 and checkedAt to the current Unix timestamp. If serenaLangDrift is absent from the existing cache, omit it (the next refresher recomputes it). If the cache file does not exist, skip this step. (Snoozed groups are already excluded by the ledger on the next real check.)

• If SHOULD_CREATE_BRANCH=true, create the branch now and remember that you created it (this determines publish behavior in Phase 8):

git checkout -b chore/update-deps-$(date +%Y-%m-%d-%H-%M)
# CREATED_NEW_BRANCH=true, used in Phase 8

Otherwise (SHOULD_CREATE_BRANCH=false), proceed on the current branch and remember that you did NOT create a new branch.

Phase 5: Wave B (per-group major bumps)

Use the Wave B groups from the apply set (the payload's wave_b minus any group the human skipped). If there are none, skip to Phase 6.

For each Wave B group, classify complexity and assign a model:

Opus (model: "opus"): react-router, react, storybook, singleton:typescript

Sonnet (model: "sonnet"): eslint, all other groups

Spawn one agent per group (or sequentially if resource-constrained), passing it these instructions:

Wave B group instructions

You are upgrading the {GROUP} dependency group from {FROM} to {TO}.

Scope. Operate on the root pnpm project only.

• Run every pnpm command from the project root. Never cd into subdirectories or use -C <path>.
• For code edits and grep-style searches, scan only app/, test/, and root config files (*.config.*, tsconfig*.json at root). Do not scan the entire repository, sibling directories may be independent pnpm projects with their own package.json/pnpm-lock.yaml, and they are out of scope for this skill.
• A directory is "out of scope" if it contains its own package.json or pnpm-lock.yaml. Skip those subtrees entirely.

1. Fetch migration guide via WebFetch using the table below. If no URL applies, scan the GitHub release notes.
2. Install the group, from project root only:
   • storybook group: run pnpm dlx storybook@latest upgrade (Storybook's own upgrade tool migrates config alongside the version bump).
   • All others: pnpm add <pkg1>@<latest> <pkg2>@<latest> ... for every group member present in root package.json.
3. Conflict check: pnpm ls 2>&1. On peer-dep error, attempt one overrides: fix in pnpm-workspace.yaml, then pnpm dedupe to apply it, a bare pnpm install won't re-resolve an overrides-only change. If still failing, revert the group and skip with reason.
4. Apply breaking changes within root scope: from the migration guide, identify code-affecting changes (renamed APIs, removed exports, config schema changes). Grep app/, test/, and root config files for affected patterns. Edit only files inside root scope.
5. Verify root package.json moved: read root package.json and confirm every group member you bumped now shows the new version. If pnpm add did not change root's spec (e.g. the dep is declared in a sibling project's package.json and not actually consumed by root code), revert the install and report the package as skipped, not a root dep. The skill does not resolve cross-project declarations; the maintainer must clean up manually. If the dep is in root package.json but has zero call sites in root scope, that's a phantom declaration: bump it anyway so the version stays current, and add a one-line note phantom: no call sites in root to the breaking-changes report so the maintainer can investigate.
6. Quality gate:

   pnpm typecheck
   pnpm lint
   pnpm test --run
   pnpm pw
   pnpm build
   

   On failure, make one remediation pass: apply fixes inferred from the migration guide, then re-run the gate once. If it still fails after that single re-run, revert the entire group and log as skipped. Do not keep iterating.

Migration guide URLs:

Report back: updated packages, breaking changes applied, any skipped reason, quality gate results.

Phase 6: Post-update override audit

For every override that was retained in Phase 0, repeat the full Phase 0 toggle test (both the peer-dep and the security-floor check, re-capturing a fresh advisory baseline against the now-updated tree) now that surrounding packages have moved. A version that landed in Wave A or Wave B may have resolved the original peer-dep conflict or carried the patched transitive dependency that made a security-floor pin obsolete. The toggle test re-resolves with pnpm dedupe, never a bare pnpm install, exactly as in Phase 0. This is the last phase that mutates the overrides: map, so the lockfile settles here: close it with the same assertion Phase 0 runs, the lockfile's overrides: block must list exactly the keys in pnpm-workspace.yaml, repairing any drift with pnpm dedupe and re-running the quality gate. Run this as a Haiku agent.

Phase 7: Final report

Build the report only from the agent reports returned to you, plus the snooze decision from Phase 1. Do not add rows from your own memory of the run.

What goes in each section:

• Updated packages: every package the Haiku agent or a Wave B agent reports as updated. Nothing else.
• Breaking changes applied: only what Wave B agents report editing in the codebase. Empty if no Wave B group ran.
• Overrides audited: only what the Phase 0 / Phase 6 audit reports. If the overrides: map was empty, write "None" and move on.
• Skipped packages: only packages that were attempted and reverted mid-run (peer-dep conflict, quality-gate failure, manual revert by an agent). Never include packages filtered out before installation by a policy rule (e.g. the ESLint 9.x cap or the release-age cooldown). Those are silent by design, surfacing them is noise that adopters see every run. When you cannot tell whether a package was policy-filtered before installation or attempted and reverted mid-run, include it in Skipped, a spurious row is recoverable but a silently dropped real failure is not. If nothing was actually skipped during the run, write "None" or omit the table.
• Snoozed (deferred this run): the companion groups the human chose to skip in the preview, with the version each was snoozed at. These quiet the statusline for 14 days (or until a newer version ships); they are not failures. Omit the section if the human chose "Update all".
• Quality gate: the gate result reported by the agents, verbatim.

If a section would be empty, write "None" rather than leaving it blank or fabricating filler.

Print the report. Do not commit.

## Migration Report

### Updated packages
| Group | Package | From | To | Type |
| --- | --- | --- | --- | --- |

### Breaking changes applied
- [group] description

### Overrides audited
- Removed: <key>, <reason>
- Retained: <key>, <reason>

### Skipped packages
| Package | Reason |
| --- | --- |

### Snoozed (deferred this run)
| Group | Snoozed at version | Resurfaces |
| --- | --- | --- |

### Quality gate
| Step | Result |
| --- | --- |

Phase 8: Publish

If nothing was updated (all packages were already up to date or all were skipped), skip this phase entirely.

Commit the update. Stage and commit the applied changes on the current branch. Write the message to a temp file first, then commit from it:

git add -A
git commit -F <commit-message-file>

The commit subject must be chore(deps): <concise summary of what moved> (use chore(deps-dev): when every bump is a devDependency). That subject is load-bearing: it triggers the dep-bump bypass in the merge gate (wiki/concepts/PR Merge Workflow.md), so the PR is turnkey-mergeable without a code-audit-frontend marker. Routing the message through a file rather than -m keeps package-manager keywords from tripping shell-hook false positives. The Wave agents already ran the full quality gate, so nothing else is owed before committing.

Then branch on where the run started.

If a new branch was created (interactive run, you were on main/master at pre-flight and branched off):

1. Push the branch:

   git push -u origin <branch-name>
   

2. Open a PR against main. Title: the commit subject. Body: the migration report rendered as markdown, via --body-file on a temp file (same false-positive reason). Capture the PR number <N> and its URL.

3. Merge when green, then clean up locally. This step runs only on a main/master run, it is what "completes the flow." Merge per wiki/concepts/PR Merge Workflow.md (the chore(deps) title clears its audit-marker gate via the dep-bump bypass):

   gh pr merge <N> --squash --delete-branch --auto
   

   --auto queues the merge so GitHub lands it once the required checks pass (or immediately if they are already green). If the repo has auto-merge disabled and gh rejects --auto, wait for the required checks to pass (gh pr checks <N>), then re-run the merge without --auto.

   gh pr merge can exit success while the merge is still queued, so verify the terminal state before touching the local checkout:

   for i in 1 2 3 4 5; do
     state=$(gh pr view <N> --json state -q .state)
     [ "$state" = "MERGED" ] && break
     sleep 30
   done
   

   • state == MERGED → clean up locally, then print the merged PR URL:

     git checkout main && git pull origin main
     git branch -D <branch-name>
     git fetch --prune origin
     

   • still not MERGED (auto-merge queued, checks not yet green) → print the PR URL and note that auto-merge is queued and will land when the checks pass. Do not delete the local branch or switch off it, the PR is still open.

If you were already on a non-main branch at pre-flight, or running in CI (no new branch was created):

1. Push the branch:

   git push
   

2. Do not open a PR and do not merge, the branch owner (the user, or the CI workflow) drives it from here.

If any git push, gh pr create, or gh pr merge above exits non-zero, print the command's error and STOP. Do not retry, force-push, or amend, a rejected push, failed PR creation, or blocked merge is the user's call to resolve (usually a manual rebase, a remote-side block, or a failing check).