diff --git a/.github/workflows/checkpoint-audit.yml b/.github/workflows/checkpoint-audit.yml
new file mode 100644
index 0000000000..0aa1c21428
--- /dev/null
+++ b/.github/workflows/checkpoint-audit.yml
@@ -0,0 +1,99 @@
+name: Checkpoint Audit
+
+on:
+  schedule:
+    - cron: "0 7 * * *" # 07:00 UTC daily (GitHub does not honor sub-daily cron reliably)
+  workflow_dispatch:
+    inputs:
+      window:
+        description: 'git --since window to audit'
+        default: '24 hours ago'
+
+permissions:
+  contents: read
+  actions: read # required for actions/upload-artifact under a restricted token (matches e2e.yml)
+
+concurrency:
+  group: checkpoint-audit-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  audit:
+    runs-on: ubuntu-latest
+    steps:
+      # The checkpoint remote (entireio/cli-checkpoints) is public, so the audit's
+      # read-only `git ls-remote` needs no credentials. If it is ever made private,
+      # set ENTIRE_CHECKPOINT_TOKEN on the audit step from a token with read access.
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          fetch-depth: 0
+
+      - name: Fetch all branches
+        run: git fetch --all --prune
+
+      # Capture the script's exit code (0 = all present, 1 = missing, 2 =
+      # remote/setup error) without failing the step, so the report, Slack, and
+      # gate steps below can distinguish "missing" from "could not run".
+      - name: Run checkpoint audit
+        id: audit
+        env:
+          AUDIT_WINDOW: ${{ github.event.inputs.window || '24 hours ago' }}
+        run: |
+          set +e
+          scripts/checkpoint-audit.sh
+          echo "code=$?" >> "$GITHUB_OUTPUT"
+          exit 0
+
+      - name: Upload audit report
+        if: always()
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+        with:
+          name: checkpoint-audit-report
+          path: |
+            checkpoint-audit-report.md
+            checkpoint-audit-report.json
+          retention-days: 7
+          if-no-files-found: ignore
+
+      # Distinct wording per outcome: exit 1 asserts missing checkpoints (a report
+      # artifact exists); exit 2 is a remote/setup failure with no report, so the
+      # alert must not claim checkpoints are missing (avoids false positives).
+      - name: Compose Slack message
+        id: msg
+        if: ${{ always() && steps.audit.outputs.code != '0' }}
+        run: |
+          if [ "${{ steps.audit.outputs.code }}" = "1" ]; then
+            echo 'text=:red_circle: *Checkpoint audit: missing checkpoints*\n\nOne or more commits reference a checkpoint that is not on the checkpoint remote. See the report artifact for the full table.' >> "$GITHUB_OUTPUT"
+          else
+            echo 'text=:red_circle: *Checkpoint audit failed to run*\n\nThe audit could not complete (remote or setup error); no report was produced. See the run log.' >> "$GITHUB_OUTPUT"
+          fi
+
+      - name: Notify Slack
+        if: ${{ always() && steps.audit.outputs.code != '0' }}
+        uses: slackapi/slack-github-action@dcb1066f776dd043e64d0e8ba94ca15cc7e1875d # v4.0.0
+        with:
+          webhook: ${{ secrets.E2E_SLACK_WEBHOOK_URL }}
+          webhook-type: incoming-webhook
+          payload: |
+            {
+              "attachments": [
+                {
+                  "color": "#d50200",
+                  "blocks": [
+                    {
+                      "type": "section",
+                      "text": {
+                        "type": "mrkdwn",
+                        "text": "${{ steps.msg.outputs.text }}\n\n<${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}|View run details>"
+                      }
+                    }
+                  ]
+                }
+              ]
+            }
+
+      - name: Fail the job on audit error
+        if: ${{ steps.audit.outputs.code != '0' }}
+        run: |
+          echo "::error::checkpoint audit exited ${{ steps.audit.outputs.code }} (1 = missing checkpoints, 2 = remote/setup error)"
+          exit 1
diff --git a/.gitignore b/.gitignore
index 0ec1a656d8..543e8b2142 100644
--- a/.gitignore
+++ b/.gitignore
@@ -71,3 +71,7 @@ tmp/
 entire-external-cp-test/
 /skills/
 /git-remote-entire
+
+# Runtime output from scripts/checkpoint-audit.sh (never commit)
+checkpoint-audit-report.md
+checkpoint-audit-report.json
diff --git a/mise.toml b/mise.toml
index a9dfb22166..34d9f02fb1 100644
--- a/mise.toml
+++ b/mise.toml
@@ -30,6 +30,10 @@ mise run test:e2e:canary
 description = "Run formatting, linting, and CI tests"
 depends = ["fmt", "lint", "test:ci"]
 
+[tasks."checkpoint:audit"]
+description = "Audit that recent commits' checkpoints exist on the checkpoint remote (set ENTIRE_CHECKPOINT_TOKEN)"
+run = "scripts/checkpoint-audit.sh"
+
 [tasks."build:windows"]
 description = "Cross-compile for Windows amd64"
 run = "CGO_ENABLED=0 GOOS=windows GOARCH=amd64 go build -o entire.exe ./cmd/entire/"
diff --git a/scripts/checkpoint-audit.sh b/scripts/checkpoint-audit.sh
new file mode 100755
index 0000000000..751c262934
--- /dev/null
+++ b/scripts/checkpoint-audit.sh
@@ -0,0 +1,183 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Audit checkpoint availability on the checkpoint remote.
+#
+# Walks every commit created within a time window across all branches, extracts
+# each `Entire-Checkpoint:` trailer, and checks whether the matching checkpoint
+# ref exists on the checkpoint remote (github.com/<CHECKPOINT_REPO>). Any commit
+# whose checkpoint ref is missing from the remote is reported with context and
+# makes the script exit non-zero.
+#
+# This catches the failure mode where a commit reaches origin but its git-refs
+# checkpoint ref (refs/entire/checkpoints/<shard>/<id>) was never pushed to the
+# checkpoint remote — the checkpoint is then unrecoverable on any other machine
+# (e.g. `entire trail resume` / `entire explain` fail with "checkpoint not found").
+#
+# Trailer parsing and ref-set membership use git's own primitives rather than
+# hand-rolled regex/shard math: `git show --format='%(trailers:...)'` parses
+# trailers (handling squash-merge commits with multiple checkpoint trailers), and
+# the checkpoint ID is simply the ref leaf, so membership is a plain string-set
+# lookup that works for both legacy-hex and ULID IDs.
+#
+# Env (all optional except the token for a private remote):
+#   ENTIRE_CHECKPOINT_TOKEN  GitHub token with read access to the checkpoint repo.
+#                            Sent as an RFC 7617 basic auth header (matching the
+#                            CLI), so it never appears in a remote URL.
+#   CHECKPOINT_REPO          owner/repo of the checkpoint remote
+#                            (default: entireio/cli-checkpoints).
+#   AUDIT_WINDOW             git `--since` window (default: "24 hours ago").
+#   AUDIT_REPORT_FILE        markdown report sink (default: checkpoint-audit-report.md).
+#   AUDIT_JSON_FILE          machine-readable report sink (default: checkpoint-audit-report.json).
+#   GITHUB_STEP_SUMMARY      if set, the markdown report is appended to it.
+#
+# Exit codes: 0 = all present, 1 = one or more checkpoints missing, 2 = setup or
+# remote error (a broken remote must never read as "0 missing").
+
+CHECKPOINT_REPO="${CHECKPOINT_REPO:-entireio/cli-checkpoints}"
+AUDIT_WINDOW="${AUDIT_WINDOW:-24 hours ago}"
+AUDIT_REPORT_FILE="${AUDIT_REPORT_FILE:-checkpoint-audit-report.md}"
+AUDIT_JSON_FILE="${AUDIT_JSON_FILE:-checkpoint-audit-report.json}"
+TOKEN="${ENTIRE_CHECKPOINT_TOKEN:-}"
+
+CHECKPOINT_URL="https://github.com/${CHECKPOINT_REPO}.git"
+
+REMOTE_IDS_FILE=$(mktemp "${TMPDIR:-/tmp}/checkpoint-audit.XXXXXX")
+ROWS_FILE=$(mktemp "${TMPDIR:-/tmp}/checkpoint-audit.XXXXXX")
+trap 'rm -f "$REMOTE_IDS_FILE" "$ROWS_FILE"' EXIT
+
+# json_str emits a JSON string literal. Git commit subjects can legally contain
+# tabs and other control characters, so escape backslash, double quote, and the
+# C0 controls that would otherwise produce invalid JSON.
+json_str() {
+  local s=${1//\\/\\\\}
+  s=${s//\"/\\\"}
+  s=${s//$'\t'/\\t}
+  s=${s//$'\r'/\\r}
+  s=${s//$'\n'/\\n}
+  s=${s//$'\b'/\\b}
+  s=${s//$'\f'/\\f}
+  printf '"%s"' "$s"
+}
+
+# 1. Enumerate the checkpoint refs present on the remote (names only, no object
+#    transfer). The ID is the ref leaf: refs/entire/checkpoints/<shard>/<ID>.
+echo "Enumerating checkpoint refs on ${CHECKPOINT_REPO} ..." >&2
+if [ -n "$TOKEN" ]; then
+  auth_b64=$(printf 'x-access-token:%s' "$TOKEN" | base64 | tr -d '\n')
+  # Standard header name/scheme casing, matching the CLI (Authorization: Basic).
+  remote_refs=$(git -c "http.extraheader=Authorization: Basic ${auth_b64}" \
+    ls-remote "$CHECKPOINT_URL" 'refs/entire/checkpoints/*') || {
+    echo "::error::failed to ls-remote ${CHECKPOINT_REPO} (check ENTIRE_CHECKPOINT_TOKEN and repo access)" >&2
+    exit 2
+  }
+else
+  remote_refs=$(git ls-remote "$CHECKPOINT_URL" 'refs/entire/checkpoints/*') || {
+    echo "::error::failed to ls-remote ${CHECKPOINT_REPO} (no ENTIRE_CHECKPOINT_TOKEN set; is the repo private?)" >&2
+    exit 2
+  }
+fi
+
+printf '%s\n' "$remote_refs" \
+  | awk '$2 ~ /^refs\/entire\/checkpoints\// { id = $2; sub(/.*\//, "", id); print id }' \
+  | sort -u > "$REMOTE_IDS_FILE"
+remote_count=$(grep -c . "$REMOTE_IDS_FILE" || true)
+
+# 2. Candidate commits: every branch commit in the window (local heads + remotes),
+#    de-duplicated while preserving order. A git-log failure (e.g. run outside a
+#    git repo) is a setup error, not "0 missing" — surface it as exit 2 rather
+#    than letting git's raw 128 escape.
+if ! commits=$(git log --branches --remotes --since="$AUDIT_WINDOW" --format='%H'); then
+  echo "::error::failed to enumerate commits (is this a git repository?)" >&2
+  exit 2
+fi
+commits=$(printf '%s\n' "$commits" | awk '!seen[$0]++')
+
+# 3. For each commit, diff its checkpoint trailers against the remote set.
+commit_count=0
+cp_count=0
+missing_count=0
+while IFS= read -r sha; do
+  [ -z "$sha" ] && continue
+  commit_count=$((commit_count + 1))
+  cps=$(git show -s --format='%(trailers:key=Entire-Checkpoint,valueonly=true)' "$sha")
+  while IFS= read -r cp; do
+    cp="${cp//[[:space:]]/}"
+    [ -z "$cp" ] && continue
+    cp_count=$((cp_count + 1))
+    if grep -Fxq "$cp" "$REMOTE_IDS_FILE"; then
+      continue
+    fi
+    missing_count=$((missing_count + 1))
+    meta=$(git show -s --format='%h%x1f%an%x1f%aI%x1f%s' "$sha")
+    short=${meta%%$'\x1f'*}; meta=${meta#*$'\x1f'}
+    author=${meta%%$'\x1f'*}; meta=${meta#*$'\x1f'}
+    cdate=${meta%%$'\x1f'*}; subject=${meta#*$'\x1f'}
+    # `|| true`: grep exits 1 when every branch is filtered out (or there are
+    # none), which would otherwise abort the whole run under `set -e`. Join with
+    # a single-char delimiter then expand to ", " — `paste -sd', '` treats the
+    # delimiter as a circular char list and would alternate "," and " ".
+    branches=$(git branch -a --contains "$sha" --format='%(refname:short)' 2>/dev/null \
+      | sed -e 's#^remotes/##' -e 's#^origin/##' \
+      | grep -v '^entire/' \
+      | awk 'NF && !s[$0]++' \
+      | paste -sd',' - \
+      | sed 's/,/, /g' || true)
+    printf '%s\x1e%s\x1e%s\x1e%s\x1e%s\x1e%s\n' \
+      "$cp" "$short" "$author" "${branches:-?}" "$cdate" "$subject" >> "$ROWS_FILE"
+  done <<EOF
+$cps
+EOF
+done <<EOF
+$commits
+EOF
+
+# 4. Render the markdown report (stdout + file + optional step summary).
+{
+  echo "# Checkpoint availability audit"
+  echo
+  echo "- Window: commits since \`${AUDIT_WINDOW}\`"
+  echo "- Checkpoint remote: \`${CHECKPOINT_REPO}\` (${remote_count} refs present)"
+  echo "- Scanned: ${commit_count} commit(s), ${cp_count} checkpoint trailer(s)"
+  echo "- **Missing from remote: ${missing_count}**"
+  echo
+  if [ "$missing_count" -gt 0 ]; then
+    echo "| Checkpoint | Commit | Author | Branch(es) | Date | Subject |"
+    echo "|---|---|---|---|---|---|"
+    while IFS=$'\x1e' read -r cp short author branches cdate subject; do
+      # Escape every free-form cell: author names and (legal) branch names can
+      # contain a pipe, which would otherwise break the markdown table.
+      author=${author//|/\\|}
+      branches=${branches//|/\\|}
+      subject=${subject//|/\\|}
+      echo "| \`${cp}\` | \`${short}\` | ${author} | ${branches} | ${cdate} | ${subject} |"
+    done < "$ROWS_FILE"
+  else
+    echo "All checkpoints referenced in the window are present on the remote. :white_check_mark:"
+  fi
+} | tee "$AUDIT_REPORT_FILE"
+
+if [ -n "${GITHUB_STEP_SUMMARY:-}" ]; then
+  cat "$AUDIT_REPORT_FILE" >> "$GITHUB_STEP_SUMMARY"
+fi
+
+# 5. Machine-readable report for the artifact.
+{
+  echo "["
+  first=1
+  while IFS=$'\x1e' read -r cp short author branches cdate subject; do
+    if [ "$first" -eq 1 ]; then first=0; else echo ","; fi
+    printf '  {"checkpoint":%s,"commit":%s,"author":%s,"branches":%s,"date":%s,"subject":%s}' \
+      "$(json_str "$cp")" "$(json_str "$short")" "$(json_str "$author")" \
+      "$(json_str "$branches")" "$(json_str "$cdate")" "$(json_str "$subject")"
+  done < "$ROWS_FILE"
+  echo
+  echo "]"
+} > "$AUDIT_JSON_FILE"
+
+if [ "$missing_count" -gt 0 ]; then
+  echo "::error::${missing_count} checkpoint(s) missing from ${CHECKPOINT_REPO}" >&2
+  exit 1
+fi
+echo "All ${cp_count} checkpoint(s) present on ${CHECKPOINT_REPO}." >&2
+exit 0