debug(agent-repo): expose reference_branches clone failure mode

Probes 7-9 (2026-05-08) all "succeeded" but with empty diffs because
AR-14a fell back to fork main: "WARNING: /workspace/reference/main/.git
not found; using fork main (may be stale)". The reference clone python
loop printed "Cloning git@..." but never "Cloned main successfully" —
no error visible either.

Most likely cause: full-history clone (post-3087ad7) is hitting some
silent failure mode (auth, fs perms, OOM, timeout). With capture_output=True
the git clone's own output was hidden.

Add explicit logging:
- python3 -u (unbuffered stdout)
- pre-loop "reference_branches loop: N entries"
- post-clone "clone returncode=N"
- always-print stdout (last 1KB) and stderr (last 1KB) from subprocess
- explicit chmod return code check
- post-clone .git existence assertion

Next probe will tell us EXACTLY what's failing.

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

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

@@ -13,9 +13,10 @@ mkdir -p /workspace/.agent-output
 # Clone reference branches (AR-12, AR-13)
 if [ -n "${REFERENCE_BRANCHES:-}" ] && [ "${REFERENCE_BRANCHES:-}" != "[]" ]; then
     echo "Cloning reference branches..."
-    echo "$REFERENCE_BRANCHES" | python3 -c "
+    echo "$REFERENCE_BRANCHES" | python3 -u -c "
 import json, sys, subprocess, os
 refs = json.load(sys.stdin)
+print(f'reference_branches loop: {len(refs)} entries')
 for ref in refs:
     name = ref.get('name', '')
     repo_url = ref.get('repo_url', '')
@@ -24,20 +25,30 @@ for ref in refs:
     print(f'Cloning {repo_url} ({branch}) -> {dest}')
     # Full clone (no --depth) so AR-14a-seeded agent branches have visible
     # ancestry when pushed back to the agent-repo. Gitea rejects shallow
-    # pushes with "shallow update not allowed". Real incident: 2026-05-08
-    # probe 7. The cost is a few extra MB on a tmpfs/PVC; acceptable.
+    # pushes with shallow-update-not-allowed. Real incident: 2026-05-08
+    # probe 7.
     result = subprocess.run(
         ['git', 'clone', '--branch', branch,
          '-c', 'core.symlinks=false', repo_url, dest],
         capture_output=True, text=True
     )
+    print(f'clone returncode={result.returncode}')
+    if result.stdout:
+        print(f'clone stdout (last 1KB): {result.stdout[-1000:]}')
+    if result.stderr:
+        print(f'clone stderr (last 1KB): {result.stderr[-1000:]}')
     if result.returncode != 0:
-        print(f'ERROR: Failed to clone {repo_url}: {result.stderr}', file=sys.stderr)
+        print(f'ERROR: Failed to clone {repo_url}', file=sys.stderr)
         sys.exit(1)
     # Strip any symlinks (security: prevent /proc/1/environ exfiltration)
     subprocess.run(['find', dest, '-type', 'l', '-exec', 'rm', '{}', ';'])
     # Make reference read-only
-    subprocess.run(['chmod', '-R', 'a-w', dest])
+    chmod_r = subprocess.run(['chmod', '-R', 'a-w', dest], capture_output=True, text=True)
+    if chmod_r.returncode != 0:
+        print(f'WARNING: chmod returned {chmod_r.returncode}: {chmod_r.stderr[:300]}')
+    if not os.path.isdir(os.path.join(dest, '.git')):
+        print(f'ERROR: clone exit 0 but {dest}/.git missing', file=sys.stderr)
+        sys.exit(1)
     print(f'Cloned {name} successfully')
 "
 fi