fix(agent-repo): harden AR-21 diff-verify against set-e/pipefail abort

The 2026-05-08 attempt-2 dogfood batch had 8/8 tasks "succeed" with
zero branches pushed. Root cause: my AR-21 diff-verification block was
running under set -euo pipefail without explicit error handling. A
single non-zero exit anywhere in the `git diff | tr | sed` pipeline
killed finalize.sh before the metadata write or push ran.

Specific risk: `git diff <REF_HEAD>..HEAD` returns non-zero when the
SHA is unreachable (e.g., shallow clone with init.sh fork-fallback
where upstream-ref wasn't fetched). pipefail then kills the pipeline,
set -e kills the script.

Fix: wrap the entire AR-21 block in `set +eo pipefail` (with explicit
`set -eo pipefail` restore at the end). Also:
- Use `${arr[@]:-}` instead of `${arr[@]}` for set -u safety on empty
  arrays
- Add `|| true` to git command substitutions (belt-and-braces)
- Use `printf` instead of `echo` for the comma-wrap (more portable)

Verified locally: when `/workspace/reference/main/.git` is absent the
block correctly skips with the existing fallback; when present and
upstream-ref is reachable, the block runs and reports DIFF_VERIFIED.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

harnesses/contexts/agent-repo/v1/finalize.sh

@@ -270,25 +270,37 @@ fi
 #   appear in the diff. Catches the inverse: an agent silently destroying or
 #   refactoring files outside the task scope (real incident: 2026-05-08 task
 #   4a2f2988 — agent stripped 9 unrelated functions; gotchas item 17/21).
+#
+# Whole block runs with set +e (and pipefail off) to ensure no diagnostic
+# pipeline failure aborts finalize before metadata can be written. We
+# explicitly check exit codes where they matter.
 DIFF_VERIFIED=true
 DIFF_MISMATCH=""
 DIFF_SUMMARY=""
+set +eo pipefail
 if [ -d /workspace/reference/main/.git ]; then
-    # All files actually changed in the agent's commit (vs upstream HEAD).
+    REF_HEAD=$(git -C /workspace/reference/main rev-parse HEAD 2>/dev/null)
-    REF_HEAD=$(git -C /workspace/reference/main rev-parse HEAD 2>/dev/null || echo "")
     if [ -n "$REF_HEAD" ]; then
-        # Files modified/added/deleted by this commit.
+        # Files modified/added/deleted by the agent vs the upstream HEAD seed.
-        DIFF_SUMMARY=$(git diff --name-only "$REF_HEAD"..HEAD 2>/dev/null | tr '\n' ',' | sed 's/,$//')
+        # Use git diff (working-tree style) plus committed changes — the
+        # agent commits via finalize.sh later, so the diff against REF_HEAD
+        # reflects total scope. `|| true` belt-and-braces against unreachable
+        # SHAs (e.g., if init.sh fell back to fork main without seeding from
+        # upstream).
+        DIFF_RAW=$(git diff --name-only "$REF_HEAD"..HEAD 2>/dev/null || true)
+        # If the .. range fails (rev-parse error) the substitution returns "".
+        # Fall back to the simpler diff against working-tree HEAD-1 (no good
+        # answer; just emit empty).
+        DIFF_SUMMARY=$(printf '%s\n' "$DIFF_RAW" | tr '\n' ',' | sed 's/,$//' || true)
 
-        # Required files must each appear in DIFF_SUMMARY.
         if [ -n "${AGENT_EXPECTED_CHANGED_FILES:-}" ]; then
             echo "Verifying required changed files: $AGENT_EXPECTED_CHANGED_FILES"
             IFS=',' read -ra _REQUIRED <<< "$AGENT_EXPECTED_CHANGED_FILES"
-            for required in "${_REQUIRED[@]}"; do
+            for required in "${_REQUIRED[@]:-}"; do
                 required="${required#"${required%%[![:space:]]*}"}"
                 required="${required%"${required##*[![:space:]]}"}"
                 [ -z "$required" ] && continue
-                if ! echo ",$DIFF_SUMMARY," | grep -qF ",$required,"; then
+                if ! printf ',%s,' "$DIFF_SUMMARY" | grep -qF ",$required,"; then
                     echo "ERROR: Required change to '$required' missing from agent's diff"
                     DIFF_VERIFIED=false
                     DIFF_MISMATCH="$DIFF_MISMATCH missing:$required"
@@ -296,15 +308,14 @@ if [ -d /workspace/reference/main/.git ]; then
             done
         fi
 
-        # Forbidden files must NOT appear in DIFF_SUMMARY.
         if [ -n "${AGENT_FORBIDDEN_CHANGED_FILES:-}" ]; then
             echo "Verifying forbidden files unchanged: $AGENT_FORBIDDEN_CHANGED_FILES"
             IFS=',' read -ra _FORBIDDEN <<< "$AGENT_FORBIDDEN_CHANGED_FILES"
-            for forbidden in "${_FORBIDDEN[@]}"; do
+            for forbidden in "${_FORBIDDEN[@]:-}"; do
                 forbidden="${forbidden#"${forbidden%%[![:space:]]*}"}"
                 forbidden="${forbidden%"${forbidden##*[![:space:]]}"}"
                 [ -z "$forbidden" ] && continue
-                if echo ",$DIFF_SUMMARY," | grep -qF ",$forbidden,"; then
+                if printf ',%s,' "$DIFF_SUMMARY" | grep -qF ",$forbidden,"; then
                     echo "ERROR: Forbidden file '$forbidden' was modified by agent"
                     DIFF_VERIFIED=false
                     DIFF_MISMATCH="$DIFF_MISMATCH forbidden:$forbidden"
@@ -321,6 +332,7 @@ if [ -d /workspace/reference/main/.git ]; then
 else
     echo "Note: /workspace/reference/main not present; skipping AR-21 diff verification"
 fi
+set -eo pipefail
 
 # AR-19: Push with retry — attempt up to PUSH_RETRIES+1 times (default 2: initial + 1 retry)
 echo "Pushing branch $BRANCH to $REPO_URL..."