update-gaia

name	update-gaia
description	Pull the latest GAIA release into this project without clobbering customizations. Three-way merge per file using .gaia/manifest.json classes. Trigger when the user clicks the statusline `Run /update-gaia` indicator or asks "update GAIA", "pull the latest GAIA", "apply the new GAIA release".

Pull the latest GAIA release into this project without clobbering customizations. Does a three-way comparison per file (adopter / baseline / latest) and respects explicit classes in .gaia/manifest.json:

• owned: GAIA controls fully. Overwrites silently if unchanged from baseline; prompts if drifted.
• shared: GAIA seeds, you customize. Emits a .gaia-merge/ patch for manual resolution on drift.
• wiki-owned: GAIA-seeded concept/decision/module wiki pages. Same drift handling as shared.
• adopter-owned (implicit): anything not in the manifest, plus sentinels like wiki/hot.md, wiki/log.md, CHANGELOG.md, .gaia/VERSION, .gaia/manifest.json. Never touched.

Backups land in .gaia-backup/<timestamp>/. Conflict patches land in .gaia-merge/.

Pre-flight: Worktree check

This wrapper changes .gaia/VERSION 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 version state from main so the user knows whether a GAIA update is even pending.

Detection (run this first, before anything else):

common_dir="$(git rev-parse --git-common-dir 2>/dev/null)"
if [ -n "$common_dir" ]; then
  case "$common_dir" in
    /*) absolute_common_dir="$common_dir" ;;
    *)  absolute_common_dir="$(pwd)/$common_dir" ;;
  esac
  main_root="$(cd "$(dirname "$absolute_common_dir")" 2>/dev/null && pwd)"
  current_root="$(git rev-parse --show-toplevel 2>/dev/null)"
  if [ -n "$main_root" ] && [ -n "$current_root" ] && [ "$main_root" != "$current_root" ]; then
    cached_line="Cached state unavailable on main; symlinks may be broken, run \`.gaia/cli/gaia setup link-worktree\` to repair."
    cache_file="$main_root/.gaia/local/cache/shared/update-check.json"
    if [ -f "$cache_file" ] && command -v jq >/dev/null 2>&1; then
      gaia_current="$(jq -r '.gaiaCurrent // ""' "$cache_file" 2>/dev/null)"
      gaia_latest="$(jq -r '.gaiaLatest // ""' "$cache_file" 2>/dev/null)"
      gaia_has_update="$(jq -r '.gaiaHasUpdate // false' "$cache_file" 2>/dev/null)"
      if [ -n "$gaia_current" ] && [ -n "$gaia_latest" ]; then
        update_phrase="not-available"
        if [ "$gaia_has_update" = "true" ]; then update_phrase="available"; fi
        cached_line="Cached on main: GAIA $gaia_current installed; latest $gaia_latest (update $update_phrase)."
      fi
    fi
    cat <<EOF
/update-gaia must run from the main checkout, not a worktree.

Worktree:       $current_root
Main checkout:  $main_root

$cached_line

Run \`cd $main_root\` then re-invoke /update-gaia.
EOF
    exit 1
  fi
fi

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, set a flag (SHOULD_CREATE_BRANCH=true) but do not create the branch yet, creation is deferred until after the Step 4 "Proceed" confirmation. Steps 1-4 can exit early (already up to date, or the user aborts); branching before then leaves an orphan chore/update-gaia-* branch when there was nothing to update.

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

Step 1: Read baseline version

cat .gaia/VERSION 2>/dev/null || echo MISSING

If the file is missing, stop and tell the user:

"No .gaia/VERSION found, this project was not scaffolded from GAIA, or the marker was deleted. Run /gaia-init on a fresh create-gaia scaffold first."

Persist the trimmed version as BASELINE (e.g., 1.0.0).

Step 2: Resolve latest release

gh release list --repo gaia-react/gaia --limit 1 --json tagName --jq '.[0].tagName'

Persist as LATEST_TAG (e.g., v1.0.1) and LATEST (strip leading v).

If gh is unavailable, fall back to:

curl -fsSL https://api.github.com/repos/gaia-react/gaia/releases/latest | jq -r .tag_name

If both fail, stop and ask the user to supply the target version explicitly.

Step 3: Compare versions

• If LATEST == BASELINE:
  • First, detect an interrupted prior run. If .gaia/VERSION differs from the last commit (git diff --quiet HEAD -- .gaia/VERSION exits non-zero, this catches a staged or unstaged bump), a previous /update-gaia already bumped the version but the update was never committed. Do not print "up to date", the bumped VERSION makes every re-run look current, so saying it dead-ends the user. Instead read the committed baseline (git show HEAD:.gaia/VERSION) for context and tell the user: the update to v$LATEST is already applied to the working tree but not committed. Review git diff and commit it (Step 10 guidance), or run git checkout -- .gaia/VERSION to discard the bump and re-run /update-gaia to start over. Exit.
  • Otherwise print "You are up to date on GAIA v$BASELINE." and exit.
• If semver(LATEST) < semver(BASELINE) → print a warning that the installed version is ahead of the latest release and exit. Never downgrade.

Step 4: Show the release notes and confirm

Show the human the full baseline-to-latest CHANGELOG range, not just the single latest tag's GitHub body, an adopter several versions behind needs every intervening entry. Read GAIA's own CHANGELOG.md at $LATEST_TAG (a plain markdown file, fetched no-auth from the raw URL, with a gh fallback) and extract every ## [x.y.z] section strictly newer than $BASELINE through $LATEST:

changelog="$(curl -fsSL "https://raw.githubusercontent.com/gaia-react/gaia/$LATEST_TAG/CHANGELOG.md" 2>/dev/null)"
if [ -z "$changelog" ] && command -v gh >/dev/null 2>&1; then
  changelog="$(gh api "repos/gaia-react/gaia/contents/CHANGELOG.md?ref=$LATEST_TAG" \
    -H "Accept: application/vnd.github.raw" 2>/dev/null)"
fi

range="$(printf '%s\n' "$changelog" | awk -v baseline="$BASELINE" -v latest="$LATEST" '
  function vcmp(a,b,   x,y,i){split(a,x,".");split(b,y,".");for(i=1;i<=3;i++){if((x[i]+0)>(y[i]+0))return 1;if((x[i]+0)<(y[i]+0))return -1}return 0}
  /^## \[Unreleased\]/           {printing=0; next}
  /^\[[^][]+\]:[[:space:]]*http/ {printing=0; next}
  /^## \[[0-9]+\.[0-9]+\.[0-9]+\]/ {
    v=$0; sub(/^## \[/,"",v); sub(/\].*/,"",v)
    printing=(vcmp(v,baseline)>0 && vcmp(v,latest)<=0)
  }
  printing {print}
')"

if [ -n "$range" ]; then
  printf '%s\n' "$range"
else
  # Fetch failed (offline, private, missing file): fall back to the single-tag
  # GitHub release body so the gate still has context.
  gh release view "$LATEST_TAG" --repo gaia-react/gaia --json body --jq .body
fi

The awk walks the version headers newest-first, prints the contiguous block from $LATEST down to (but not including) $BASELINE, and drops the [Unreleased] block and the bottom link-reference list. Print the range to the user. Then use AskUserQuestion:

• Question: "Update GAIA from v$BASELINE to $LATEST_TAG?"
• Options: Proceed / Abort.

On Abort, exit cleanly with no filesystem changes.

If SHOULD_CREATE_BRANCH=true, create and switch to the branch now that the user has confirmed:

git checkout -b chore/update-gaia-$(date +%Y-%m-%d-%H-%M)

Otherwise stay on the current branch.

Step 4b: Prune prior-run artifacts

Three gitignored directories accumulate across updates: .gaia-backup/, .gaia/local/cache/shared/update-gaia/, and .gaia-merge/. Prune the prior runs' leftovers here, at the start of a confirmed update and before this run creates any of its own artifacts (Step 5 populates the cache, Step 7 creates $BACKUP_DIR), so the current run's fresh safety net is never touched. This runs only after the Step 4 Proceed, so an abort, an already-up-to-date exit, and the interrupted-prior-run case Step 3 surfaces (whose backups and patches are still in flight) never reach it.

# .gaia-backup/: prior runs' pre-overwrite copies. Once an update is committed,
# git history is the durable recovery, so prior backups are redundant. This run
# creates its own $BACKUP_DIR in Step 7.
rm -rf .gaia-backup

# .gaia/local/cache/shared/update-gaia/: keep the baseline tarball (v$BASELINE
# is this run's baseline, reused by Step 5 instead of re-downloading). Delete
# every other cached tag dir. The loop only ever touches tag dirs here,
# update-check.json and serena-guard/ live one level up at shared/,
# structurally outside this glob.
if [ -d .gaia/local/cache/shared/update-gaia ]; then
  for d in .gaia/local/cache/shared/update-gaia/*/; do
    [ -d "$d" ] || continue
    [ "$(basename "$d")" = "v$BASELINE" ] && continue
    rm -rf "$d"
  done
fi

# .gaia-merge/: conflict patches + .notes the operator resolves by hand (Step
# 11). Remove only when empty; a populated dir holds unresolved action items, so
# never delete it, warn and name the leftovers instead.
if [ -d .gaia-merge ]; then
  if [ -n "$(ls -A .gaia-merge 2>/dev/null)" ]; then
    echo "Heads up: .gaia-merge/ still holds unresolved patches from a prior run, NOT deleted:"
    ls -A .gaia-merge
    echo "Resolve or delete them by hand, then re-run /update-gaia."
  else
    rmdir .gaia-merge
  fi
fi

Model selection

After the user confirms, determine the model for the execution agent:

• Compare LATEST major vs BASELINE major (leading integer).
• Major bump → spawn an Opus agent (model: "opus").
• Minor or patch bump → spawn a Sonnet agent (model: "sonnet").

Spawn the agent for Steps 5–10, passing BASELINE, LATEST, and LATEST_TAG as context.

---

Steps 5–10 (execution agent)

Step 5: Fetch baseline and latest tarballs

Cache under .gaia/local/cache/shared/update-gaia/ (gitignored) so repeated runs don't redownload:

mkdir -p .gaia/local/cache/shared/update-gaia
for tag in "v$BASELINE" "$LATEST_TAG"; do
  dir=".gaia/local/cache/shared/update-gaia/$tag"
  [ -d "$dir" ] && continue
  mkdir -p "$dir"
  if ! gh release download "$tag" \
      --repo gaia-react/gaia \
      --pattern "gaia-${tag}.tar.gz" \
      --dir "$dir" \
    || ! tar -xzf "$dir/gaia-${tag}.tar.gz" -C "$dir" --strip-components=1; then
    rm -rf "$dir"
    echo "FETCH_FAILED $tag"
  fi
done

BASELINE_DIR=".gaia/local/cache/shared/update-gaia/v$BASELINE", LATEST_DIR=".gaia/local/cache/shared/update-gaia/$LATEST_TAG".

The block prints FETCH_FAILED <tag> for any tag whose download or extraction did not complete, and removes the partial cache dir so a re-run retries cleanly. On any FETCH_FAILED, stop, do not proceed to Step 6:

• FETCH_FAILED $LATEST_TAG: the latest release is unreachable (network, auth, or a missing release asset). Tell the user, then re-run once it is reachable.
• FETCH_FAILED v$BASELINE: the baseline tarball is unavailable (older release, pre-manifest). The three-way merge needs a baseline, so stop and explain the adopter can manually cherry-pick changes by comparing their project to $LATEST_DIR.

Step 6: Load the latest manifest

LATEST_MANIFEST="$LATEST_DIR/.gaia/manifest.json"

Iterate keys of .files. For each <path>, <class> entry, apply the decision table below. Track counts per outcome for the summary.

Load the region declarations. A few shipped files carry a marker-delimited region whose body is machine-generated: a shipped command rewrites it, so an adopter who runs that command diverges from the release copy without ever hand-editing the file. The manifest declares each one under an optional top-level regions key, and Step 7 compares a declared path with its region masked out instead of whole-file.

REGION_AWARE=true
if [ "${GAIA_UPDATE_NO_REGIONS:-}" = "1" ]; then
  REGION_AWARE=false
fi

REGION_DECLS='[]'
BASELINE_REGION_DECLS='[]'
if [ "$REGION_AWARE" = true ]; then
  REGION_DECLS="$(jq -c '.regions // []' "$LATEST_MANIFEST" 2>/dev/null || echo '[]')"
  BASELINE_REGION_DECLS="$(jq -c '.regions // []' \
    "$BASELINE_DIR/.gaia/manifest.json" 2>/dev/null || echo '[]')"
fi

Each declaration is {id, startMarker, endMarker, paths[], regenerate: {interpreter, operand, args[]}}. Build a lookup of declared path to declaration so the Step 7 walk can test each path in one step, and track the region bucket described in Step 7 as you go.

• Parse defensively. There is no manifest validation on the adopter side; this flow reads raw JSON and iterates the file map. A regions key that is absent, an empty list, or unparseable all mean the same thing: zero declarations, no oracle call, no regeneration, and every file classified by the unmodified whole-file comparison exactly as it is without region awareness.
• Ignore a malformed declaration, do not abort. A declaration that is not an object, is missing id / startMarker / endMarker / regenerate / paths, carries an empty or whitespace-only marker, or repeats an id already seen, is skipped: its paths take the unmodified whole-file comparison, no regeneration runs for it, and it is recorded for the Step 9 summary. Track these as regions.malformedDeclarations[].
• The off switch. GAIA_UPDATE_NO_REGIONS=1 set in the environment for one run makes the flow load zero declarations. Step 9 states that region awareness was off, and the update otherwise behaves exactly as it does without it. This is the adopter-facing remedy for a bad declaration or an oracle bug in the field: it needs no edit to the write-blocked .gaia/manifest.json and no flag on the command.
• Dropped declarations. Any id the baseline manifest declared that the latest manifest does not is a dropped declaration. Its paths return to the unmodified whole-file comparison, so a conflict that region awareness had been absorbing comes back. Step 9 must name it, so the return is announced rather than discovered. Track as regions.droppedDeclarations[].
• Region awareness governs the next update, not this one. The merge walk is prose the execution agent holds from the adopter's installed copy of this file, and the walk overwrites that copy partway through the run. Nothing re-reads instruction prose out of the staged release. So the first update that installs region awareness still runs the walk that predates it, and a declared path the adopter has already regenerated still lands in conflicts[] on that one run. Resolving the two subcommands from $LATEST_DIR does not shorten the lag; it only makes a newly shipped subcommand reachable at all. The release CHANGELOG announces this with a one-time regeneration the adopter runs by hand.

Step 7: Three-way merge

Apply the decision table directly, there is no CLI for this step.

Design-system sentinel check (runs before the manifest walk):

Read the established field from the working-tree wiki/concepts/Design System.md frontmatter:

design_established=false
if [ -f "wiki/concepts/Design System.md" ] && grep -qE '^established:[[:space:]]*true' "wiki/concepts/Design System.md"; then
  design_established=true
fi

If design_established=true, the adopter has committed their design system. Both wiki/concepts/Design System.md and .claude/rules/design-baseline.md are effectively adopter-owned from this point forward. Add both paths to skip[] and exclude them from the manifest walk entirely: no overwrite, no conflict patch, no backup. The adopter's content is the source of truth.

If design_established=false, apply the normal decision table to both files as their manifest class dictates.

Setup:

BACKUP_DIR=".gaia-backup/$(date +%Y%m%d-%H%M%S)"
mkdir -p .gaia-merge "$BACKUP_DIR"

# Snapshot whether the installed audit-ci.yml already declares default_mode,
# captured BEFORE the Step 7c merge can write the key. The Step 10 opt-in nudge
# reads this; gating on the post-merge file state would let the merge pre-silence
# the nudge on the very run that should surface it.
had_default_mode_before_merge=false
if [ -f .gaia/audit-ci.yml ] && grep -qE '^[[:space:]]*default_mode[[:space:]]*:' .gaia/audit-ci.yml; then
  had_default_mode_before_merge=true
fi

Persist had_default_mode_before_merge for Step 10.

Track seven lists plus a package.json sub-report internally (UpdateMergeReport):

{
  overwrite: string[];   // owned files overwritten with latest
  skip: string[];        // no change needed; left alone
  merge: string[];       // clean shared/wiki-owned merges written into the working tree
  add: string[];         // new files copied from latest
  removed: string[];     // adopter deleted a baseline file; deletion respected, left absent
  delete: string[];      // files removed upstream; surfaced but NOT auto-deleted
  adopterActions: Array<{ // Step 9: documented, opt-in follow-ups the merge leaves
    subject: string;      //   to the adopter (a dep GAIA dropped that you still have,
    command?: string;     //   a delete[] file still present), recovered from the
    changelog: string;    //   release CHANGELOG's adopter-action convention. Advisory.
  }>;
  conflicts: Array<{
    path: string;
    class: 'owned' | 'shared' | 'wiki-owned';
    patch_path: string;  // .gaia-merge/<path>.patch
  }>;
  packageJson: {         // field-aware result for package.json (Step 7a)
    applied: string[];      // managed keys GAIA changed that the adopter still tracked at the baseline pin, written to the working tree
    conflicts: string[];    // managed keys GAIA changed but the adopter independently re-pinned, left as the adopter's, noted
    suggestions: string[];  // managed keys GAIA added, or changed but the adopter had removed, surfaced opt-in, never applied
    notes_path?: string;    // .gaia-merge/package.json.notes when conflicts or suggestions exist
  };
  pnpmWorkspace: {       // field-aware result for pnpm-workspace.yaml (Step 7b)
    applied: string[];      // managed keys / overrides+allowBuilds entries GAIA changed that the adopter still tracked, written to the working tree
    conflicts: string[];    // managed keys / entries GAIA changed but the adopter independently re-pinned, left as the adopter's, noted
    suggestions: string[];  // managed keys / entries GAIA added, or changed but the adopter had removed, surfaced opt-in, never applied
    notes_path?: string;    // .gaia-merge/pnpm-workspace.yaml.notes when conflicts or suggestions exist
  };
  auditCiYml: {          // field-aware result for .gaia/audit-ci.yml (Step 7c)
    applied: string[];      // managed scalar knobs / audit_authors entries GAIA changed that the adopter still tracked, PLUS any auditors roster member GAIA added or changed that the adopter hasn't diverged (a roster addition is applied here, not suggested, see Step 7c), written to the working tree
    conflicts: string[];    // knobs / entries / roster members GAIA changed but the adopter independently diverged, left as the adopter's, noted
    suggestions: string[];  // scalar knobs / audit_authors entries GAIA added, or changed but the adopter had removed, surfaced opt-in, never applied
    notes_path?: string;    // .gaia-merge/audit-ci.yml.notes when conflicts or suggestions exist
  };
  regions: {             // declared generated regions (Step 6 load, Step 7 oracle, Step 7d regeneration)
    // A distinct bucket, NOT an extension of adopterActions[]. That array's
    // `changelog` field is mandatory and is populated only from
    // convention-anchored CHANGELOG bullets; a regeneration failure has no
    // changelog source, so it does not fit. Do not merge the two.
    awarenessOff: boolean;         // GAIA_UPDATE_NO_REGIONS=1 was set for this run
    declarationsLoaded: number;
    droppedDeclarations: string[]; // region ids the baseline declared and latest does not
    fallbacks: Array<{             // declared paths region awareness did not normalize as intended
      path: string;
      reason: 'absent-markers' | 'malformed-markers' | 'oracle-failed';
    }>;
    malformedDeclarations: Array<{index: number; reason: string}>;
    regen?: RegenRegionsReport;    // absent when Step 7d did not run
    rewrittenPaths: string[];      // regen.ran[].rewrote, flattened
    supersededPatches: string[];   // pre-existing .gaia-merge patches for declared paths
    unregeneratedPaths: string[];  // every declared path of a skipped / refused / failed region
  };
}

Iterate every <path>: <class> entry in $LATEST_MANIFEST's .files object, except package.json, pnpm-workspace.yaml, and .gaia/audit-ci.yml, all three are handled field-aware below (package.json in Step 7a, pnpm-workspace.yaml in Step 7b, .gaia/audit-ci.yml in Step 7c). A whole-file cmp/diff can't separate adopter identity and intentional removals from the real upstream delta; pnpm-workspace.yaml is a mixed file (GAIA-authored supply-chain / resolution settings plus adopter-extensible overrides and allowBuilds maps) that drifts the moment an adopter adds one override; and .gaia/audit-ci.yml is a mixed file (GAIA-authored scalar knobs, the adopter-extensible audit_authors login=mode string, and the auditors roster list, which is GAIA-authored and adopter-extensible at once) that drifts the moment a developer commits one per-author entry or a roster member is added on either side. Skip all three during this walk.

Let A = working-tree <path>, B = $BASELINE_DIR/<path>, L = $LATEST_DIR/<path>. Use cmp -s for equality; mkdir -p before writing.

Match in declared order, first matching row wins. Baseline presence (B) is the discriminator for a missing working-tree file: A missing with B also missing means the file is genuinely new in the latest release and gets added; A missing with B present means the adopter deliberately deleted a file that shipped in their baseline, so the deletion is respected and the file is left absent. The B ≅ L row (no upstream change) short-circuits every class before any conflict is declared, an adopter-drifted file the release never touched has nothing to merge, so it stays as-is and emits no patch.

Class	Condition	Action	List
any	A missing and B missing (genuinely new in latest)	Copy L → <path>	add[]
any	A missing and B exists (adopter deleted it)	No-op, respect the deletion, leave absent	removed[]
owned	B missing (A exists; release newly owns this path)	Back up A to $BACKUP_DIR/<path>; copy L → <path>	overwrite[]
any	B ≅ L (no upstream change)	No-op	skip[]
any	A ≅ B (no adopter drift)	Back up A to $BACKUP_DIR/<path>; copy L → <path>	owned → overwrite[]; shared / wiki-owned → merge[]
any	A ≅ L (adopter already at latest)	No-op	skip[]
owned	A ≠ B and A ≠ L	diff -u "$A" "$L" > .gaia-merge/<path>.patch	conflicts[]
shared / wiki-owned	A ≠ B and A ≠ L	diff -u "$A" "$L" > .gaia-merge/<path>.patch	conflicts[]

Declared generated regions. A path that appears in one of the Step 6 declarations takes a single oracle call in place of the whole-file cmp -s comparisons, so a divergence confined to the machine-generated region does not read as adopter drift.

Presence triage still runs first, and it is unchanged. The first two rows of the table above (A missing with B missing → add[]; A missing with B present → deletion respected, removed[]) and the owned + B missing row resolve before the oracle is ever consulted. A path the adopter deleted, a path the release no longer ships, and a path absent from the baseline are settled there: no oracle call, and no regeneration in Step 7d either.

For a declared path that survives triage:

region_json="$("$LATEST_DIR/.gaia/cli/gaia" update merge-region \
  --baseline "$BASELINE_DIR/<path>" \
  --latest "$LATEST_DIR/<path>" \
  --current "<path>" \
  --start-marker "<declaration startMarker>" \
  --end-marker "<declaration endMarker>" \
  --json 2>/dev/null)" || region_json=''

Resolve the subcommand from $LATEST_DIR, never from the working-tree copy of the CLI. An adopter whose installed binary predates the subcommand cannot reach it any other way, and that is the only reason the rule exists.

Then read .verdict and take the matching row:

verdict	Row it takes
no-upstream-change	No-op, skip[]
no-adopter-drift	Back up A to $BACKUP_DIR/<path>; copy L → <path>. owned → overwrite[], shared / wiki-owned → merge[]
already-latest	No-op, skip[]
conflict	Write the normalized patch (below), conflicts[]

These are the same rows the table above produces, in the same order, applied to normalized content instead of raw content. There is no new row.

The normalized conflict patch. The oracle emits the normalized bodies because nothing else in this flow can parse a region. Build the patch from them, never from the raw files:

printf '%s' "$region_json" | jq -r '.normalized.current' > "$tmp_current"
printf '%s' "$region_json" | jq -r '.normalized.latest'  > "$tmp_latest"
diff -u -L "<path>" -L "<path> (latest)" "$tmp_current" "$tmp_latest" \
  > ".gaia-merge/<path>.patch"
rm -f "$tmp_current" "$tmp_latest"

GAIA's conflict patches are advisory reading: the flow reads them and walks the adopter through the decision per file (see "Handling results" below), so a normalized patch that no longer applies cleanly as a machine patch is not a defect. What the adopter reads is exactly the divergence they caused, and no line of it comes from either side's region body.

Marker anomalies. Read .markers and record a fallback for the Step 9 summary under a reason that keeps two distinct states apart:

• .markers.bailed is true → reason malformed-markers. Some side's marker pair is duplicated, unbalanced, or out of order, so the oracle normalized no side, its verdict is the row the unmodified whole-file comparison produces, and it still exited 0. Report the path.
• .markers.bailed is false and some side reports "scan": "absent" → reason absent-markers. That side carries no marker pair at all, which is the expected pre-region state, not a defect. Normalization still applied per side. Report it as informational and keep it distinct from a malformed one.

Oracle failure. When the command exits non-zero (region_json empty: a CLI predating the subcommand, an unreadable file, a missing flag), fall back to the unmodified whole-file comparison for that path. Never fall back to a forced conflict patch. Record reason oracle-failed, and say plainly in Step 9 what it means: that path has returned to its pre-region behavior, which for an adopter carrying a region-only divergence is exactly the conflict region awareness exists to remove. Do not present the fallback as harmless.

Superseded patches. Before the walk, note any .gaia-merge/<declared path>.patch left over from a prior run. Step 4b deliberately never deletes a populated .gaia-merge/, so a stale patch from a pre-region run survives and would send the adopter hand-resolving a region this run handles for them. Record these in regions.supersededPatches[] and name them in Step 9 as superseded.

After iterating the manifest, collect deletions: files present under $BASELINE_DIR with no corresponding key in $LATEST_MANIFEST's .files. Split each by working-tree presence: a file still present in the working tree goes to delete[] (surfaced for the user to confirm, never auto-removed); a file the adopter has already removed (working-tree absent) is already reconciled, so record it in removed[] count-only with no prompt. This mirrors the per-key table's delete vs removed split for upstream-dropped files.

Handling results:

• overwrite[], skip[], merge[], add[], removed[]: report counts only, no per-file narrative. Do not read file bytes.
• delete[]: ask the user before removing each path.
• conflicts[]: read the patch at .gaia-merge/<path>.patch and walk the user through the decision per file.
• packageJson: populated by Step 7a. The applied[] keys are already written to the working tree (report counts only); walk the user through conflicts[] (re-pinned keys) and mention suggestions[] (added / removed-then-changed deps) as opt-in, both detailed in .gaia-merge/package.json.notes.
• pnpmWorkspace: populated by Step 7b. Same shape and handling as packageJson, detailed in .gaia-merge/pnpm-workspace.yaml.notes.
• auditCiYml: populated by Step 7c. Same shape and handling as packageJson, detailed in .gaia-merge/audit-ci.yml.notes.
• regions: populated by Step 6 (declarations), this walk (verdicts and fallbacks), and Step 7d (regeneration). Report counts and the named follow-ups in Step 9; there is no notes file and no per-file narrative here beyond what Step 9 prints.

Step 7a: Field-aware package.json merge

package.json is classed shared, but a whole-file three-way merge produces pure noise for it: every adopter diverges it at init (gaia-init rewrites name / description / author and resets version), and GAIA bumps its own version on every release, so A ≠ B, A ≠ L, and B ≠ L all hold on every release, and the generic table emits a full-file conflict patch dominated by identity fields no adopter wants from GAIA. Merge it at JSON-key granularity instead, acting only on the genuine upstream delta B → L.

Let A = working-tree package.json, B = $BASELINE_DIR/package.json, L = $LATEST_DIR/package.json.

Adopter-owned keys, never compared, merged, or patched. Every top-level key except the managed sections below is the adopter's, left exactly as-is: name, version, description, author, private, type, bin, sideEffects, and anything else. Identity drift is invisible to this step.

Managed sections, three-way merged per entry:

• Object sections, merged per entry key: dependencies, devDependencies, scripts, engines.
• Scalar / whole-value keys, merged as a single value: packageManager.

Resolution, overrides, and build-approval (allowBuilds) settings live in pnpm-workspace.yaml, classed owned and merged by the generic Step 7 walk, not here. pnpm 11 reads them only from there; the package.json pnpm field and a top-level overrides key are not pnpm-managed package.json sections.

For each managed entry key k (within its section), with Bk / Lk / Ak its value in baseline / latest / adopter:

Condition on k	Meaning	Action	Bucket
in B and L, Bk == Lk	GAIA didn't change it	No-op. The adopter's value stands, kept, re-pinned, or removed.	,
in B and L, Bk != Lk, adopter has k and Ak == Bk	GAIA changed the pin; adopter still at baseline	Apply Lk to the working tree	applied[]
in B and L, Bk != Lk, adopter has k and Ak != Bk	GAIA changed it; adopter re-pinned independently	Conflict. Leave Ak; note both pins. Never silently override an adopter pin.	conflicts[]
in B and L, Bk != Lk, adopter removed k	GAIA changed a dep the adopter dropped	Suggestion. Do not re-add. Note as opt-in.	suggestions[]
in L, not in B	GAIA added it	Suggestion. Do not auto-insert. Note as opt-in.	suggestions[]
in B, not in L	GAIA removed it	If the adopter still has k, leave it (adopter's choice).	,

The load-bearing row is the first one: a dependency the adopter removed (present in B, absent from A) is never re-added unless GAIA itself changed it this release and the adopter opts in. The default everywhere is to respect the adopter's value. This is the JSON-key analog of the file-level "respect adopter deletions" rule the generic table already enforces.

The last row is the load-bearing one for Step 9: GAIA removed k (in B, not in L) but the adopter still has it, so the merge leaves it (the adopter's choice). That no-op is invisible by design, the adopter is never told GAIA dropped the dependency. Step 9 cross-references these GAIA-removed-but-still-present deps against the release CHANGELOG's adopter-action convention and offers an opt-in pnpm remove suggestion. The merge itself never removes the dependency; only the user can.

Compute the per-key verdicts with jq (covers the object sections):

jq -n \
  --slurpfile a package.json \
  --slurpfile b "$BASELINE_DIR/package.json" \
  --slurpfile l "$LATEST_DIR/package.json" '
  ($a[0]) as $A | ($b[0]) as $B | ($l[0]) as $L
  | [["dependencies"],["devDependencies"],["scripts"],["engines"]] as $sections
  | [ $sections[] as $sp
      | (($B | getpath($sp)) // {}) as $bs
      | (($L | getpath($sp)) // {}) as $ls
      | (($A | getpath($sp)) // {}) as $as
      | (($bs + $ls) | keys_unsorted | unique)[] as $k
      | { section: ($sp | join(".")), key: $k, baseline: $bs[$k], latest: $ls[$k], adopter: $as[$k],
          verdict:
            (if ($bs | has($k)) and ($ls | has($k)) then
               (if $bs[$k] == $ls[$k] then "noop"
                elif ($as | has($k) | not) then "suggest-removed"
                elif $as[$k] == $bs[$k] then "apply"
                else "conflict" end)
             elif ($ls | has($k)) then "suggest-add"
             else "noop" end) }
      | select(.verdict != "noop") ]'

Apply the same rule to the scalar packageManager by hand: B == L → no-op; B != L and A == B → apply; B != L and A != B → conflict; in L only → suggest-add; in B only → no-op.

Apply clean changes (applied[]): edit the single line for k in the working-tree package.json so its value becomes Lk, using the Edit tool, preserve the adopter's formatting and key order. Do not reserialize the file with jq write-back; that reorders keys and buries the real change in noise.

Record conflicts + suggestions: if either bucket is non-empty, write a human-readable .gaia-merge/package.json.notes listing, per key: the section, the key, the adopter / baseline / latest values, and the recommended action. Set notes_path. This file is informational, the adopter reconciles re-pin conflicts by hand and accepts or ignores suggestions. It is not a diff -u patch and is not added to the file-level conflicts[] bucket.

Net effect:

• Version-only release (no managed-key delta) → identity ignored, zero applied/conflicts/suggestions → clean skip, no notes file. Fixes the every-release noise.
• Dep-bump release → only the entries GAIA actually changed (and that the adopter still tracks) are applied; re-pin conflicts and added/removed-dep suggestions go to the notes file, never re-adding a dependency the adopter removed, never overwriting an adopter pin.

Step 7b: Field-aware pnpm-workspace.yaml merge

pnpm-workspace.yaml is classed shared, but it is a mixed file, so a whole-file three-way merge produces the same noise package.json does. It carries GAIA-authored settings (minimumReleaseAge, trustPolicy, trustPolicyExclude, minimumReleaseAgeExclude, publicHoistPattern, savePrefix, strictPeerDependencies) and adopter-extensible maps (overrides, allowBuilds). pnpm 11 reads dependency overrides and build approvals only from here, so any adopter who adds a single override drifts the file and eats a full-file conflict patch on every release that touches it. Merge it at YAML-key / map-entry granularity instead, acting only on the genuine upstream delta B → L.

Let A = working-tree pnpm-workspace.yaml, B = $BASELINE_DIR/pnpm-workspace.yaml, L = $LATEST_DIR/pnpm-workspace.yaml.

Presence triage first (older baselines predate pnpm 11 and have no pnpm-workspace.yaml). Match the first row that applies; only the last row runs the field-aware merge:

Condition	Action
L missing	Upstream dropped the file; fold into the Step 7 deletion sweep (delete[]). Skip 7b.
A missing and B missing	Genuinely new; copy L → pnpm-workspace.yaml. Record in add[]. Skip 7b.
A missing and B exists	Adopter deleted it; respect the deletion, leave absent. Record in removed[]. Skip 7b.
A exists and B missing	No baseline to field-merge against; diff -u A L > .gaia-merge/pnpm-workspace.yaml.patch. Surface as a conflict. Skip 7b.
A, B, L all exist	Run the field-aware merge below.

Compute the per-key / per-entry verdicts with the bundled CLI (it parses all three files with js-yaml and never writes the YAML):

.gaia/cli/gaia update merge-workspace \
  --baseline "$BASELINE_DIR/pnpm-workspace.yaml" \
  --latest "$LATEST_DIR/pnpm-workspace.yaml" \
  --current pnpm-workspace.yaml \
  --json

The command exits non-zero with a structured error if any file is missing or not valid YAML (for example the adopter introduced a syntax error). On a non-zero exit, fall back to a whole-file conflict patch (diff -u A L > .gaia-merge/pnpm-workspace.yaml.patch) and surface it as a conflict; do not proceed with the JSON path.

The JSON report is { applied, conflicts, suggestions }. Each item is { kind: 'key' | 'entry', section?, key, baseline?, latest?, adopter?, reason? }. The CLI iterates only keys(B) ∪ keys(L) per managed key and per overrides / allowBuilds entry, so an adopter-only override or build approval is never visited, never clobbered. The seven GAIA-managed keys are compared whole-value; the two map sections are compared per entry. Both use the identical verdict table as Step 7a (apply / conflict / suggest-add / suggest-removed).

Apply clean changes (applied[]): for each item, edit the working-tree pnpm-workspace.yaml so the key's (or entry's) value becomes latest, using the Edit tool. Preserve the file's comments, key order, and quote style; change only the value text. Do not reserialize the file (js-yaml dump strips every comment). A whole-value list change replaces the list block; a scalar or map-entry change edits the single line.

Record conflicts + suggestions: if either bucket is non-empty, write a human-readable .gaia-merge/pnpm-workspace.yaml.notes listing, per item: the section (if any), the key, the adopter / baseline / latest values, and the recommended action. Set notes_path. This file is informational; the adopter reconciles re-pin conflicts by hand and accepts or ignores suggestions. It is not a diff -u patch and is not added to the file-level conflicts[] bucket.

Net effect:

• No managed-key delta (overrides / allowBuilds / settings unchanged by the release) → zero applied/conflicts/suggestions → clean skip, no notes file.
• Settings or override change → only the keys / entries GAIA actually changed (and that the adopter still tracks) are applied; re-pin conflicts and added/removed suggestions go to the notes file, never re-adding a key the adopter removed, never overwriting an adopter override.

Step 7c: Field-aware .gaia/audit-ci.yml merge

.gaia/audit-ci.yml is classed shared, but it is a mixed file like pnpm-workspace.yaml, carrying three kinds of content: GAIA-authored scalar knobs (gate_label, budget_seconds, max_turns, push_fixes, default_mode, override_label, the retrigger_workflows list); the adopter-extensible audit_authors string, a space-separated login=mode list each developer appends their own pair to via /setup-gaia; and the auditors roster list, GAIA-authored and adopter-extensible at once (GAIA ships and updates its own members, an adopter can add their own alongside them). A whole-file three-way merge emits a full-file conflict patch the moment one developer commits an audit_authors entry or an adopter adds their own roster member, so merge it at YAML-key / per-entry granularity instead, acting only on the genuine upstream delta B → L.

Let A = working-tree .gaia/audit-ci.yml, B = $BASELINE_DIR/.gaia/audit-ci.yml, L = $LATEST_DIR/.gaia/audit-ci.yml.

Presence triage first (older baselines predate this file): identical to Step 7b's triage table, substituting .gaia/audit-ci.yml for pnpm-workspace.yaml (its fallback patch is .gaia-merge/audit-ci.yml.patch, and each "Skip 7b" reads "Skip 7c"). Only the last row (A, B, L all exist) runs the field-aware merge below.

Compute the per-key / per-entry verdicts with the bundled CLI (it parses all three files with js-yaml and never writes the YAML):

.gaia/cli/gaia update merge-audit-ci \
  --baseline "$BASELINE_DIR/.gaia/audit-ci.yml" \
  --latest "$LATEST_DIR/.gaia/audit-ci.yml" \
  --current .gaia/audit-ci.yml \
  --json

The command exits non-zero with a structured error if any file is missing or not valid YAML. On a non-zero exit, fall back to a whole-file conflict patch (diff -u A L > .gaia-merge/audit-ci.yml.patch) and surface it as a conflict; do not proceed with the JSON path.

The JSON report is { applied, conflicts, suggestions }. Each item is { kind: 'key' | 'entry', section?, key, baseline?, latest?, adopter?, reason? }. The CLI iterates only keys(B) ∪ keys(L) per managed scalar key, per audit_authors login, and per auditors roster member name, so an adopter-only developer entry or an adopter-added roster member is never visited, never clobbered. The seven managed knobs are compared whole-value; audit_authors is parsed into per-login entries (the login compared case-insensitively, matching the resolver's case-fold) and compared per login; auditors is parsed into per-member entries (the name compared exactly, not case-folded, a member name is an agent filename, not a login) and each member's whole mapping (globs, scope, push_fixes, default) is compared and applied as a unit, never glob-by-glob. All three sections use the identical verdict table (apply / conflict / suggest-add / suggest-removed), with one deliberate exception: for auditors only, a member present in latest and absent from baseline resolves to apply, not suggest-add. Every other section treats that row as an opt-in suggestion the adopter must act on; a roster member is a capability the adopter cannot opt into if it never arrives, so a new GAIA-authored member (e.g. code-audit-github-workflows) is written straight into the adopter's file rather than surfaced as something they might miss. An adopter's own roster member is still never visited, and an adopter's edit to a GAIA-authored member is still a conflict, not silently overwritten.

Apply clean changes (applied[]): for each item, edit the working-tree .gaia/audit-ci.yml so the key's (or entry's) value becomes latest, using the Edit tool. Preserve the file's comments, key order, and quote style; change only the value text. For an audit_authors entry item, edit that login's =mode token inside the existing audit_authors string; do not rewrite the whole string or reorder the other developers' entries. For an auditors roster item: if the member already exists in the working tree, edit its globs: / scope: / push_fixes: / default: fields in place to match latest; if it is a new member (the added-row exception above), append a whole new - name: ... list item to the auditors: list, matching the indentation and key order of its neighbors. Do not reserialize the file.

Record conflicts + suggestions: if either bucket is non-empty, write a human-readable .gaia-merge/audit-ci.yml.notes listing, per item: the section (if any), the key, the adopter / baseline / latest values, and the recommended action. Set notes_path. This file is informational; it is not a diff -u patch and is not added to the file-level conflicts[] bucket.

Net effect:

• No managed-key delta (knobs, any shipped audit_authors entries, and the roster all unchanged by the release) → zero applied/conflicts/suggestions → clean skip, no notes file. An adopter whose only divergence is their committed audit_authors entries or their own added roster member never sees a conflict.
• Reader safe-defaults absent keys: an adopter whose installed file predates these keys is fine, the reader defaults override_label=run-audit and audit_authors= empty; a missing default_mode now falls back to local. The merge adds the keys. This is a real behavior change for the pre-default_mode cohort, their next merge moves them from CI-audited to local-audited; see the Step 10 opt-in nudge for what to tell them.
• A GAIA-authored roster addition always lands in applied[], not suggestions[]. This is the one section whose added-row verdict diverges from every other merged section (scalar knobs, audit_authors), by design (see above): the alternative would mean a new GAIA-authored auditor never reaches an existing adopter's file at all.

Step 7d: Regenerate declared regions

This step must run after Step 7c and before Step 8, and the ordering is the whole point of the step. A declared region's body is derived from the adopter's own post-merge tree, and for the shipped audit-remit region that source is the auditors roster in .gaia/audit-ci.yml, which Step 7c merges. Regenerating before Step 7c would derive every region from the pre-merge roster, so a GAIA-authored member this release just added would be missing from the region the adopter ends up with, and the roster check would fail on a file this run had supposedly just made current. Running before Step 8 keeps the whole merge, including this write, inside the window .gaia/VERSION still names the baseline, so an interrupted run stays resumable.

if [ "$REGION_AWARE" = true ] && [ "$REGION_DECLS" != "[]" ]; then
  regen_json="$("$LATEST_DIR/.gaia/cli/gaia" update regen-regions \
    --manifest "$LATEST_MANIFEST" \
    --root . \
    --backup-dir "$BACKUP_DIR" \
    ${conflicted_flags} \
    ${absent_path_flags} \
    ${skip_region_flags} \
    --json 2>/dev/null)" || regen_json=''
fi

Resolve this subcommand from $LATEST_DIR for the same reason the oracle is resolved there. The regeneration program is the opposite: --root . points the runner at the adopter's working tree, so it runs the copy of the program the merge walk just wrote.

Build the three repeatable flag groups from this run's own lists:

• ${conflicted_flags}: one --conflicted <path> per declared path this run placed in conflicts[]. A path left in conflict is not regenerated on this run; the adopter has not resolved it yet, and regenerating would discard whatever they are about to choose. They get the literal command as a Step 9 follow-up instead.
• ${absent_path_flags}: one --absent-path <path> per declared path this run placed in removed[]. A path the adopter deliberately deleted must not be resurrected, and the runner cannot infer that on its own: mid-run, a deliberately deleted file and an ordinary pre-region absence look identical on disk. Passing them explicitly is what makes "deletions are respected" a property of the mechanism rather than a coincidence of one writer's behavior.
• ${skip_region_flags}: one --skip-region <id> per region whose inputs this run did not reconcile. Today that means Step 7c fell back to a whole-file conflict patch for .gaia/audit-ci.yml, so the roster the audit-remit region derives from is not the merged one.

Suppression is region-granular. One --conflicted or --absent-path hit suppresses the whole region, not just that path, and the region lands in skipped[] with the reason naming the paths responsible. Its sibling declared paths may already have been overwritten with the release copy by the walk, so they now carry GAIA's version of the region rather than the adopter's. Every declared path of a skipped, refused, or failed region goes into regions.unregeneratedPaths for Step 9, whichever merge-walk list the path itself landed in.

The runner exits 0 for every refusal, skip, spawn failure, and non-zero program exit; only unusable flags or an unusable manifest are a non-zero exit. A failed or refused regeneration never fails the update. If regen_json is empty, record that and continue: the expected cause is a CLI that predates the subcommand, which is exactly the state of the very first region-aware run. Do not stop the update.

Persist the parsed report as regions.regen, and flatten ran[].rewrote into regions.rewrittenPaths for Step 9. The report shape:

type RegenRegionsReport = {
  backedUp: string[];   // declared paths the runner copied into $BACKUP_DIR itself
  confined: Array<{     // writes outside a region's declared paths
    action: 'removed' | 'reported' | 'restored';
    path: string;
    regionId: string;
  }>;
  failed: Array<{argv: string[]; kind: 'exit' | 'spawn'; message: string; regionId: string; status?: number}>;
  ran: Array<{argv: string[]; regionId: string; rewrote: string[]}>;
  refused: Array<{argv?: string[]; kind: 'declaration' | 'operand'; reason: string; regionId: string}>;
  skipped: Array<{argv: string[]; reason: string; regionId: string}>;
};

Every bucket Step 9 prints a command for carries its own argv, because the region id alone cannot be turned back into a command. The one exception is a kind: 'declaration' refusal: a declaration too malformed to name an interpreter and an operand has no command, so argv is absent and Step 9 says so rather than inventing one.

What the step guarantees, and what it does not:

• The regeneration is authoritative. A declared region's body is machine-authored, so regeneration overwrites whatever sits between the markers, including an adopter's hand edits inside them. That is by design. Step 9 names every path whose region this run rewrote, so the overwrite is stated rather than silent.
• Writes are confined and backed up. The runner writes nothing outside a region's declared path set: a write inside the region's own directories is reverted to what it held before the run, and a write anywhere else in the tree, which has no pre-image to restore from, is reported instead. It also copies every declared path it is about to rewrite into $BACKUP_DIR first, unless the merge walk already backed that path up.
• The operand guard is well-formedness, not security. The runner refuses an operand that is absolute, carries a parent-directory segment, resolves through a symlink out of the repository, or is not an exact key of the same manifest's shipped file map. This guards against a stale, corrupt, or hand-edited declaration. It is not a defense against anyone who controls the manifest: the flow already extracts and runs the release tarball's bundled tool, so a manifest that could not be trusted would be the smaller problem. Do not describe it as a security control to the adopter.

Step 8: Count trailer invalidations

The version bump itself is deferred to Step 9 (after the summary prints) so an interrupted run stays resumable, see that step for the rationale. First, while BASELINE still names the installed version, count open PRs whose GAIA-Audit trailer is stamped with it. The upcoming bump invalidates them, they re-run the full CI audit on their next push:

INVALIDATED_COUNT=0
if command -v gh >/dev/null 2>&1; then
  OLD_VERSION="$BASELINE"
  pr_list=$(gh pr list --state open --json number,headRefOid 2>/dev/null || true)
  if [ -n "$pr_list" ]; then
    while IFS= read -r sha; do
      [ -z "$sha" ] && continue
      msg=$(git log -1 --format='%B' "$sha" 2>/dev/null || true)
      if echo "$msg" | grep -qE "^GAIA-Audit:[[:space:]]+${OLD_VERSION}[[:space:]]+[0-9a-f]{40}"; then
        INVALIDATED_COUNT=$((INVALIDATED_COUNT + 1))
      fi
    done < <(echo "$pr_list" | jq -r '.[].headRefOid' 2>/dev/null || true)
  fi
else
  INVALIDATED_COUNT="unknown"
fi

Persist INVALIDATED_COUNT for Step 9.

Step 8b: Migrate SPEC artifacts to per-SPEC folders

SPEC artifacts live in per-SPEC folders: .gaia/local/specs/<spec_id>/SPEC.md (archived: .gaia/local/specs/archived/<spec_id>/). .gaia/local/specs/** is adopter-owned data the three-way merge never touches, so the freshly-updated runbooks reference the folder layout while the adopter's existing specs may still be flat files. Run the migration script to fold any flat specs into the folder layout. It is idempotent, a no-op when specs are already foldered or none exist, so run it unconditionally:

spec_folderize_out=$(bash .specify/extensions/gaia/lib/spec-folderize.sh 2>&1)
spec_folderize_rc=$?

Parse the result for the Step 9 summary:

• The script writes spec-folderize: migrated <n> SPEC artifact(s) ... to stderr on a successful migration. Persist <n> as SPECS_MIGRATED. On a no-op (already foldered or no specs) the script exits 0 with a nothing to migrate line, set SPECS_MIGRATED=0.
• Exit code 4 is a migration conflict: a flat SPEC-<id>.md and a folder <id>/SPEC.md both exist for the same id. The script names both conflicting paths on stderr and changes nothing. Do not swallow this and do not auto-resolve it. Capture the conflicting ids/paths from $spec_folderize_out, set SPECS_MIGRATED="conflict", and surface it in Step 9 as a blocking action item the user must reconcile by hand.
• Any other non-zero exit (2 usage, 3 unresolvable repo root) is a script-invocation error. Do not hard-stop here, that would discard the Step 9 summary covering every file already merged. Capture $spec_folderize_out, set SPECS_MIGRATED="error", and route it through Step 9 as a blocking action item (same handling as the exit-4 conflict).

Step 9: Summary

Print a table:

GAIA update: v$BASELINE → $LATEST_TAG

  Overwritten:  <n>
  Added:        <n>
  Removed:      <n>  (files you deleted; left absent, deletion respected)
  Skipped:      <n>
  Conflicts:    <n>  (see .gaia-merge/)
  Deleted:      <n>  (removed upstream; surfaced, not auto-deleted)
  package.json: <a> applied, <c> conflicts, <s> suggestions  (field-aware; see .gaia-merge/package.json.notes)
  pnpm-workspace.yaml: <a> applied, <c> conflicts, <s> suggestions  (field-aware; see .gaia-merge/pnpm-workspace.yaml.notes)
  audit-ci.yml: <a> applied, <c> conflicts, <s> suggestions  (field-aware; see .gaia-merge/audit-ci.yml.notes)
  Regions:      <r> regenerated, <f> failed, <s> skipped, <x> refused  (see notes below)
  Region fallbacks: <n>  (declared paths compared whole-file this run)
  Pre-region paths: <n>  (declared paths not yet carrying a region)
  Backed up:    <n>  (see .gaia-backup/<timestamp>/)
  Specs migrated: <n>  (flat .gaia/local/specs files folded into per-SPEC folders)
  Trailer invalidations: <n>  (open PRs stamped v$BASELINE will re-audit on next push)

When all three package.json counts are zero, render that row as package.json: no managed-key changes (clean skip) and omit the notes reference. Apply the same rule to the pnpm-workspace.yaml row: pnpm-workspace.yaml: no managed-key changes (clean skip) when all three of its counts are zero. If 7b fell back to a whole-file conflict patch (presence triage or a parse failure), render the row as pnpm-workspace.yaml: whole-file conflict (see .gaia-merge/pnpm-workspace.yaml.patch) instead. Apply the same two rules to the audit-ci.yml row: audit-ci.yml: no managed-key changes (clean skip) when all three counts are zero, or audit-ci.yml: whole-file conflict (see .gaia-merge/audit-ci.yml.patch) when 7c fell back.

The three region rows. Counts come from regions.regen (ran / failed / skipped / refused) and regions.fallbacks. Render them like this:

• regions.awarenessOff is true → replace all three rows with the single line Regions: awareness off for this run (GAIA_UPDATE_NO_REGIONS=1); every declared path used the whole-file comparison.
• regions.declarationsLoaded is 0 and awareness is on → Regions: none declared by this release, and omit the other two rows.
• Every count zero → Regions: all declared regions current (no regeneration needed).
• Omit the Region fallbacks row and the Pre-region paths row individually whenever that row's own count is zero.

The fallback row counts only malformed-markers and oracle-failed. Those two are the paths that genuinely took the unmodified whole-file comparison. An absent-markers path was normalized per side, so counting it in a row that tells the adopter it was compared whole-file states something false and collapses a distinction that has to stay visible: a wholly absent marker pair is the expected state of a file that has never been regenerated, while a malformed one is a defect somebody has to fix. Absent-marker paths get the separate Pre-region paths row, which carries no alarm.

Use SPECS_MIGRATED for the Specs migrated row. If it is "conflict", emit the row as Specs migrated: conflict, see action item below and, after the table, print a blocking action item naming the conflicting ids/paths from $spec_folderize_out:

Action required: SPEC migration could not complete. A flat SPEC-<id>.md and a folder <id>/SPEC.md exist for the same id: . Resolve by hand (keep one, remove the other), then re-run bash .specify/extensions/gaia/lib/spec-folderize.sh to finish the migration. The freshly-updated runbooks reference the folder layout, so leaving this unresolved breaks SPEC tooling.

If SPECS_MIGRATED is "error", emit the row as Specs migrated: error, see action item below and, after the table, print a blocking action item carrying the script-invocation failure from $spec_folderize_out:

Action required: SPEC migration could not run, the spec-folderize.sh script errored: <$spec_folderize_out>. The GAIA file merge completed and is summarized above; only the SPEC-artifact migration was skipped. Fix the reported error, then re-run bash .specify/extensions/gaia/lib/spec-folderize.sh to finish the migration. The freshly-updated runbooks reference the folder layout, so leaving this unresolved breaks SPEC tooling.

If INVALIDATED_COUNT is "unknown", emit instead:

  Trailer invalidations: unknown  (gh unavailable, open PRs with GAIA-Audit stamps may re-audit)

If INVALIDATED_COUNT is greater than 0, also print after the table:

Note: $INVALIDATED_COUNT open PR(s) carry a GAIA-Audit trailer stamped with v$BASELINE. On their next push, CI re-runs the full audit (one extra billing cycle per PR). This is intentional, a newer GAIA agent version may catch issues the prior version missed. To minimize re-audit churn, merge or close these PRs before updating GAIA.

Documented adopter actions (opt-in). Two merge outcomes leave the adopter with a follow-up the three-way merge deliberately will not perform: a dependency GAIA dropped this release that the adopter still has (the Step 7a "GAIA removed it; adopter still has it" no-op, left in place by design) and files removed upstream still in the working tree (delete[]). Both are silent or bare, the agent knows what changed but surfaces no why. Recover the intent from the release CHANGELOG and offer an opt-in suggestion.

Read $LATEST_DIR/CHANGELOG.md (already on disk from Step 5, no extra fetch) and extract the ## [x.y.z] sections strictly newer than $BASELINE through $LATEST with the same range-walk awk as Step 4 (see that block), with one difference: here the awk reads the file as a positional argument (awk -v baseline="$BASELINE" -v latest="$LATEST" '…' "$LATEST_DIR/CHANGELOG.md") rather than from piped stdin.

Within that range, match only convention-anchored entries: bullets under a ### Removed or ### Changed heading that carry an explicit **Action required:** line and/or a literal pnpm command in backticks. Key on the heading plus that anchored phrasing; do not free-parse arbitrary prose (the convention is documented in CHANGELOG.md). For each match, take the literal command (the backtick-quoted pnpm …) and the subject it names, then gate it on whether the action still applies to this adopter and record the survivors in adopterActions[]:

• A pnpm remove <pkg> / pnpm uninstall <pkg> action applies only when <pkg> is still present in the adopter's package.json (exactly the Step 7a removal no-op). If the adopter already removed it, skip, there is nothing to do.
• An action naming a file that also appears in delete[] applies only while that file is present.

When adopterActions[] is non-empty, print a recommendation block after the table:

Suggested cleanup (optional). This release documents adopter actions that /update-gaia leaves to you:

• GAIA removed react-router-dom this release, run pnpm remove react-router-dom? (still in your package.json)

These are advisory. Run a command only if you want it.

This stays opt-in. The CHANGELOG context upgrades a silent no-op into a suggestion; it never changes the merge's "respect the adopter's choice" behavior and never auto-removes a dependency or deletes a file. This mirrors the Step 8b SPEC-migration action item: surfaced for the user, never auto-resolved.

Generated regions. Print each of the following after the table, whenever it applies. Each one reports a state the adopter cannot see any other way, so none may be dropped for brevity.

1. Rewritten regions. Name every path in regions.rewrittenPaths, and state that those files now intentionally differ from the release copy because their region is derived from this adopter's own roster. Anything that later reports them as drifted is describing the intended state.

2. Failed or refused regenerations. One entry per region, carrying the literal argument vector to run by hand, rendered from that entry's argv (for the region GAIA ships today that renders as bash .gaia/scripts/write-audit-remits.sh). Report a spawn failure distinctly from a non-zero exit: a spawn failure means the interpreter itself could not be launched, while a non-zero exit means the program ran and refused, and the two have different remedies. Report per region rather than per path, because one command covers every path in the region, and the shipped writer aggregates per-member failures into a single non-zero exit after rewriting the members that did succeed.

   A kind: 'declaration' refusal carries no argv, and that is correct. A declaration too malformed to name an interpreter and an operand has no command to hand over. Print the defect, and state plainly that this release's declaration is unusable and there is nothing for the adopter to run: the remedy is upstream, not in their tree. Never fabricate a command for it.

3. Skipped regenerations. Name the region, the reason the runner gave, and the literal command from its argv.

   The follow-up command is always the regeneration program, never a re-run of the CLI's own regeneration subcommand. argv renders as bash .gaia/scripts/write-audit-remits.sh, which the adopter can paste into any shell once they have resolved whatever suppressed it. A CLI invocation is unusable as printed text: the release-resolved form names a cache directory that exists only for the duration of the run, and the working-tree form is banned by the release-resolution rule in Step 7. The regeneration program is deliberately exempt from that rule, because it is resolved from the adopter's own tree by design.

4. Un-regenerated regions on otherwise-clean paths. Report every path in regions.unregeneratedPaths as carrying an un-regenerated region, rather than as a plain skip, and say what that means: the file's generated block does not match what this adopter's own configuration would produce.

   Do not scope this to skip[]. Regeneration is region-granular, so one conflicted path suppresses its whole region while a sibling declared path may have been cleanly overwritten with the release copy and now sits in overwrite[] or merge[]. That sibling carries GAIA's roster-derived region instead of the adopter's, and scoping the warning to skip[] is exactly the case where the adopter would be told nothing while their region is stale.

5. Whole-file fallbacks. Every entry in regions.fallbacks, grouped by reason. For oracle-failed and malformed-markers, state that the path returned to pre-region behavior for this run, so a divergence confined to its generated region reads as ordinary drift and can produce a conflict patch the adopter did not cause. For absent-markers, state that the file simply does not carry the region yet, which is the expected state before the first regeneration, and that nothing is wrong.

6. Dropped declarations. Name every id in regions.droppedDeclarations and say that its paths return to whole-file comparison from now on, so a conflict that region awareness had been absorbing is announced here instead of surprising them on a later release.

7. Malformed declarations. Name each entry in regions.malformedDeclarations with its index and reason. The adopter cannot fix these (the declaration ships with the release), so pair them with the off switch: GAIA_UPDATE_NO_REGIONS=1 disables region awareness for a run if a bad declaration is causing trouble.

8. Superseded patches. Name every entry in regions.supersededPatches and say the pre-existing patch is superseded by this run's handling of that path, so the adopter deletes it instead of hand-resolving a region the run already reconciled.

9. Audit gate clearance. The paths carrying a shipped region are audit gate machinery, so a regeneration write on a resumed update changes files the gate has already cleared. Clearance markers earned on an earlier push to the same pull request are invalidated, and the dispatched Code Audit Team members have to be re-spawned on the new HEAD.

10. Confined writes. When regions.regen.confined is non-empty, name each entry with its action: restored and removed are writes the regeneration made outside its declared paths and the runner undid, reported is a write outside the region's own directories that had no pre-image to restore from and was left in place. A reported entry is the one the adopter has to look at, and a wholly new untracked directory surfaces as the directory itself rather than as its individual files.

The merge walk is complete and the summary is recorded, so finalize the version. Write the new version and refresh the manifest:

echo "$LATEST" > .gaia/VERSION
GAIA_MANIFEST_WRITE=release cp "$LATEST_DIR/.gaia/manifest.json" .gaia/manifest.json

The manifest copy carries the GAIA_MANIFEST_WRITE= marker, a bare edit is blocked by .claude/hooks/block-manifest-write.sh, and this wholesale replace is the release-only write the guard exempts. This refreshes .gaia/manifest.json from the release copy so the next /update-gaia has the right baseline. Unresolved conflict patches, re-pin notes, or a SPEC-migration action item do not block this bump, they are follow-ups the user resolves against the already-recorded update; .gaia/VERSION tracks the file merge, which is done.

Now that the bump has landed, record the transition:

.gaia/cli/gaia ping --event update --from "$BASELINE" --to "$LATEST" || true

This ping records the version transition for adoption analytics and is best-effort, it never gates the update or its resumability.

Deferring the bump to this point (rather than before the walk) keeps an interrupted run resumable: any abort during the walk (user cancels, disk error) leaves .gaia/VERSION at BASELINE, and because the merge is idempotent (already-merged files match latest and skip), a re-run picks up cleanly. Overwritten files are safe, their prior state is in .gaia-backup/. Step 3 catches the remaining window where the bump landed but the user has not yet committed.

Then bust the update-check cache so the SessionStart prompt reflects the post-update state on the next session. Use the Write tool to overwrite .gaia/local/cache/shared/update-check.json with gaiaCurrent set to $LATEST, gaiaLatest set to $LATEST, gaiaHasUpdate set to false, outdatedCount set to 0, and checkedAt set to the current Unix timestamp. Preserve serenaLangDrift from the existing cache (read it first); if it is absent, omit it (the next refresher recomputes it). If the cache file does not exist, skip this step.

The next SessionStart hook fires the background refresher; the session after that sees no GAIA update available.

Step 10: Next steps for the user

Tell the user:

1. Review any conflict patches in .gaia-merge/ and reconcile manually. Delete the patch file once resolved. If .gaia-merge/package.json.notes or .gaia-merge/pnpm-workspace.yaml.notes exists, reconcile the re-pin conflicts and decide on the suggestions, then delete it.
2. If the package.json or pnpm-workspace.yaml merge applied any change (a dependency / packageManager bump, or an override / allowBuilds / resolution-setting change), run pnpm install to sync pnpm-lock.yaml before the quality gate.
3. If any region regeneration failed, was refused, or was skipped, running the command named in the Step 9 report is a follow-up the adopter owns. Resolve whatever suppressed it first (the conflict patch for that path, most often), then run the command and re-run the roster check to confirm the region is current.
4. Run the quality gate per wiki/decisions/Quality Gate.md to verify the updated code still passes.
5. Inspect the diff (git diff) before committing.
6. When satisfied, commit with chore: update GAIA to $LATEST_TAG.

Opt-in nudge (only when had_default_mode_before_merge is false). Show this line only when the pre-Step-7 snapshot found no default_mode key in the installed .gaia/audit-ci.yml, i.e. the adopter's config predates the per-author audit mode. Gate on the snapshot, NOT the post-merge file state: the Step 7c merge may have just added the key, and gating on the current file would pre-silence the nudge on the very run that should surface it. Once the adopter's own config carries default_mode (a later run's snapshot finds it), the nudge no longer fires.

New: per-author audit mode. The code-audit-frontend now runs locally at merge time by default, falling back to CI only for a pinned per-author override or a fork PR. This changes your merges from CI-audited to local-audited starting now. Run /setup-gaia to set the team policy, either keep CI-audited, or record your own per-author preference.

Do not auto-commit on behalf of the user, they need to review the changes first.

---

Steps 11–12 (orchestrator, after the user commits)

The execution agent's work ends at Step 10, it returns its UpdateMergeReport and the orchestrator relays the summary. Steps 11-12 run in the orchestrator, not the spawned agent: they depend on the Step 10 commit, which is the user's manual action and lands after the one-shot agent has already returned. Run them once that commit exists.

Step 11: Open a pull request

After the Step 10 commit lands, /update-gaia must not leave the branch stranded, open a PR so the update can be reviewed and merged.

The orchestrator waits for the user to confirm the Step 10 commit landed before pushing, the git rev-list guard below is only a backstop for the empty-branch case, not a replacement for that confirmation.

Push the branch and open a PR, but only if it has no open PR already, a re-run of /update-gaia on the same branch updates the existing PR instead of duplicating it:

branch="$(git branch --show-current)"

# The update must be committed first (Step 10). No commits ahead of main → finish Step 10.
if [ "$(git rev-list --count main.."$branch" 2>/dev/null || echo 0)" -eq 0 ]; then
  echo "Nothing committed ahead of main, commit the update (Step 10) before opening a PR."
  exit 0
elif ! git push -u origin "$branch"; then
  echo "Push failed, resolve the push error, then open the PR manually: $branch → main."
else
  existing="$(gh pr list --head "$branch" --state open --json number --jq '.[0].number // empty' 2>/dev/null)"
  if [ -n "$existing" ]; then
    echo "PR #$existing already open for $branch, pushed the new commit to it."
  else
    gh pr create --base main --head "$branch" \
      --title "chore: update GAIA to $LATEST_TAG" \
      --body "Pulls GAIA $LATEST_TAG into the project. Per-file outcomes are in the update summary above."
  fi
fi

If gh is unavailable or errors, tell the user to open the PR manually: $branch → main.

Step 12: Refresh a stale CI audit workflow

.github/workflows/code-review-audit.yml is not synced by the manifest walk (Steps 6-7); the audit workflow installs and updates through its own template, not a manifest class. A project that enabled GAIA CI on an older release therefore keeps whatever audit workflow shipped then, frozen, even after this update pulls a newer template. That stale copy is the root of an ordering trap: if this update's payload makes has_source=true (a dependency or config bump), CI runs a full audit under the stale workflow on the PR just opened, which cannot earn a clean GAIA-Audit stamp, and the operator then has to run /setup-gaia by hand to refresh it (a second commit that self-mod-skips). Refreshing the workflow inside this update PR collapses that into a single, expected self-mod-skip.

The audit workflow is adopter-tunable: an adopter may have customized it (self-hosted runners, extra secrets wiring, concurrency, extra steps), so it is refreshed via a 3-way classify that never clobbers real edits. The audit template is static (no render), so the three inputs are files already on disk:

• A = the installed workflow, .github/workflows/code-review-audit.yml
• L_old = the prior release's template, $BASELINE_DIR/.gaia/cli/templates/workflows/code-review-audit.yml.tmpl
• L_new = this release's template, $LATEST_DIR/.gaia/cli/templates/workflows/code-review-audit.yml.tmpl

gaia setup-ci check-audit-drift classifies them and the SKILL acts on the verdict: missing (CI not installed → silent no-op, this is the opt-in guard), in_sync (already current, or this release did not touch the template → no-op), clean (A == L_old, stale but un-customized → safe to overwrite), or conflict (A matches neither template, or the baseline template is unavailable → never auto-write).

# $BASELINE (pre-update version) and $LATEST_TAG carry from the run, as in
# Step 11. The release tarball cache from Step 5 still holds both templates.
BASELINE_DIR=".gaia/local/cache/shared/update-gaia/v$BASELINE"
LATEST_DIR=".gaia/local/cache/shared/update-gaia/$LATEST_TAG"
audit_tmpl=".gaia/cli/templates/workflows/code-review-audit.yml.tmpl"
audit_wf=".github/workflows/code-review-audit.yml"

audit_state="$(.gaia/cli/gaia setup-ci check-audit-drift \
  --baseline "$BASELINE_DIR/$audit_tmpl" \
  --latest "$LATEST_DIR/$audit_tmpl" \
  --json 2>/dev/null | jq -r '.state // "unknown"' 2>/dev/null || echo unknown)"

case "$audit_state" in
  clean)
    # Stale but un-customized: overwrite with the new template and land it in
    # the update PR so CI sees the refreshed workflow from the start. The
    # commit stages only a workflow YAML (no ts/tsx/css), so the Quality Gate
    # has nothing to check.
    cp "$LATEST_DIR/$audit_tmpl" "$audit_wf"
    git add "$audit_wf"
    if git commit -m "chore: re-render code-review-audit.yml for $LATEST_TAG" && git push; then
      echo "Refreshed $audit_wf from the $LATEST_TAG template and pushed it to the update PR."
    else
      echo "Refreshed $audit_wf from the $LATEST_TAG template; commit and push it to the update PR manually."
    fi
    cat <<EOF
Expectation: re-rendering $audit_wf makes this update PR self-modifying, so claude-code-action's workflow-validation guardrail refuses to run the audit on it. CI self-mod-skips the audit, one expected skip instead of a wasted full audit under the stale workflow plus a manual /setup-gaia step. This does NOT earn a clean CI GAIA-Audit stamp; the merge still relies on a local audit marker / trailer or the out-of-scope bypass (see PR Merge Workflow). This is a UX/ordering cleanup, not a path to a clean stamp.
EOF
    ;;
  conflict)
    # Adopter customized the workflow, or the baseline template is missing.
    # Never auto-write: emit a sidecar patch (installed -> latest template) and
    # defer to a manual refresh, mirroring the Step 7 conflict handling.
    mkdir -p .gaia-merge
    diff -u "$audit_wf" "$LATEST_DIR/$audit_tmpl" \
      > ".gaia-merge/code-review-audit.yml.patch" || true