loki-mode 9.52.0 → 9.53.0

package/SKILL.md

@@ -3,7 +3,7 @@ name: loki-mode
 description: Autonomous spec-driven build system with a built-in trust layer. It does not call work done until it is verified (RARV-C closure loop, 8 quality gates, completion council, verified-completion evidence gate). Triggers on "Loki Mode". Takes a spec (PRD, GitHub issue, OpenAPI doc, etc.) to deployed product with minimal human intervention. Provider-agnostic. Requires --dangerously-skip-permissions flag.
 ---
 
-# Loki Mode v9.52.0
+# Loki Mode v9.53.0
 
 **You are an autonomous agent. You make decisions. You do not ask questions. You do not stop.**
 
@@ -470,4 +470,4 @@ See `CHANGELOG.md` entries [7.5.7], [7.5.8], [7.5.13] for the per-fix list and r
 
 ---
 
-**v9.52.0 | [Autonomi](https://www.autonomi.dev/) flagship product | ~410 lines core**
+**v9.53.0 | [Autonomi](https://www.autonomi.dev/) flagship product | ~410 lines core**

package/VERSION

@@ -1 +1 @@
-9.52.0
+9.53.0

package/autonomy/completion-council.sh

@@ -19,6 +19,12 @@
 #   - Multi-agent debate: Voting beats unanimous (+13.2%), KS adaptive stopping
 #   - NVIDIA ToolOrchestra: Efficiency metrics for agent tool use
 #
+# Inline Python (D7): the council runs with the cwd inside the agent's repo, so
+# every "python3 -c" / "python3 -" here runs -E (a PYTHONPATH empty component
+# would load a committed sitecustomize.py) and drops '' and '.' from sys.path
+# before any other import (a committed json.py would print the verdict).
+# Pinned by tests/moat/p2-honest-verdict.sh P2.council-readers-not-shadowed.
+#
 # Environment Variables:
 #   LOKI_COUNCIL_ENABLED          - Enable completion council (default: true)
 #   LOKI_COUNCIL_SIZE             - Number of council members (default: 3)
@@ -371,7 +377,7 @@ council_track_iteration() {
     _COUNCIL_ITERATION="${ITERATION_COUNT:-0}" \
     _COUNCIL_FILES_CHANGED="$files_changed" \
     _COUNCIL_DIFF_HASH="$combined_hash" \
-    python3 -c "
+    python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, os
 state_file = os.environ['_COUNCIL_STATE_FILE']
 try:
@@ -453,7 +459,7 @@ _uncertainty_state_path() {
 # Read uncertainty.json (or emit a default object if missing/corrupt) to stdout.
 _uncertainty_read_state() {
     local file="$1"
-    _UNC_FILE="$file" python3 -c "
+    _UNC_FILE="$file" python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, os
 f = os.environ['_UNC_FILE']
 default = {
@@ -487,7 +493,7 @@ _uncertainty_write_state() {
     dir="$(dirname "$file")"
     mkdir -p "$dir" 2>/dev/null || true
     tmp="${file}.tmp.$$"
-    if _UNC_PAYLOAD="$payload" _UNC_TMP="$tmp" python3 -c "
+    if _UNC_PAYLOAD="$payload" _UNC_TMP="$tmp" python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, os
 payload = os.environ['_UNC_PAYLOAD']
 tmp = os.environ['_UNC_TMP']
@@ -539,7 +545,7 @@ uncertainty_should_escalate() {
              _UNC_SPLIT_ROUNDS="$split_rounds" \
              _UNC_NOCHANGE_MIN="$nochange_min" \
              _UNC_RING_SIZE="$ring_size" \
-             python3 -c "
+             python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, os
 
 prior = json.loads(os.environ['_UNC_PRIOR'])
@@ -826,7 +832,7 @@ council_vote() {
                 local budget_exceeded=false
                 if [ "$total_issue_count" -gt 0 ] && [ "$COUNCIL_ERROR_BUDGET" != "0.0" ] && [ "$COUNCIL_ERROR_BUDGET" != "0" ]; then
                     # Check if non-blocking issue ratio exceeds the error budget
-                    budget_exceeded=$(_NB="$non_blocking_count" _TOTAL="$total_issue_count" _BUDGET="$COUNCIL_ERROR_BUDGET" python3 -c "
+                    budget_exceeded=$(_NB="$non_blocking_count" _TOTAL="$total_issue_count" _BUDGET="$COUNCIL_ERROR_BUDGET" python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import os
 nb = int(os.environ['_NB'])
 total = int(os.environ['_TOTAL'])
@@ -918,7 +924,7 @@ print('true' if ratio > budget else 'false')
     _COUNCIL_REJECT="$reject_count" \
     _COUNCIL_ITERATION="${ITERATION_COUNT:-0}" \
     _COUNCIL_THRESHOLD="$effective_threshold" \
-    python3 -c "
+    python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, os
 from datetime import datetime, timezone
 state_file = os.environ['_COUNCIL_STATE_FILE']
@@ -1036,7 +1042,7 @@ council_write_transcript() {
     _MEMBERS_DIR="$COUNCIL_STATE_DIR/votes/iteration-${iteration}" \
     _THRESHOLD="$effective_threshold" \
     _OUT="$transcript_file" \
-    python3 -c "
+    python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, os, pathlib, re
 
 iteration_id = os.environ['_IID']
@@ -1214,7 +1220,7 @@ EVIDENCE_SECTION
         local queue_file=".loki/queue/${queue}.json"
         if [ -f "$queue_file" ]; then
             local count
-            count=$(_QUEUE_FILE="$queue_file" python3 -c "import json, os; print(len(json.load(open(os.environ['_QUEUE_FILE']))))" 2>/dev/null || echo "?")
+            count=$(_QUEUE_FILE="$queue_file" python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]; import json, os; print(len(json.load(open(os.environ['_QUEUE_FILE']))))" 2>/dev/null || echo "?")
             echo "- ${queue}: $count tasks" >> "$evidence_file"
         fi
     done
@@ -1287,7 +1293,7 @@ EVIDENCE_SECTION
     elif [ -f ".loki/verification/playwright-results.json" ]; then
         echo "" >> "$evidence_file"
         echo "## Playwright Smoke Test Results" >> "$evidence_file"
-        _PW_RESULTS=".loki/verification/playwright-results.json" python3 -c "
+        _PW_RESULTS=".loki/verification/playwright-results.json" python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, os
 try:
     d = json.load(open(os.environ['_PW_RESULTS']))
@@ -1375,7 +1381,7 @@ council_checklist_gate() {
     # council_heldout_gate at the ship gate, and surfacing them in this gate's
     # block report would leak their identity back into the build loop.
     local gate_result
-    gate_result=$(_RESULTS_FILE="$results_file" _WAIVERS_FILE="$waivers_file" _HELDOUT_FILE="$heldout_file" python3 -c "
+    gate_result=$(_RESULTS_FILE="$results_file" _WAIVERS_FILE="$waivers_file" _HELDOUT_FILE="$heldout_file" python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, sys, os
 
 results_file = os.environ['_RESULTS_FILE']
@@ -1438,13 +1444,13 @@ else:
         local timestamp
         timestamp=$(date -u +"%Y-%m-%dT%H:%M:%SZ")
         local failures_json
-        failures_json=$(_FAILURES="$failures" python3 -c "
+        failures_json=$(_FAILURES="$failures" python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, os
 items = os.environ['_FAILURES'].split('|')
 print(json.dumps(items))
 " 2>/dev/null || echo '[]')
         local critical_count
-        critical_count=$(_FAILURES="$failures" python3 -c "
+        critical_count=$(_FAILURES="$failures" python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import os
 print(len(os.environ['_FAILURES'].split('|')))
 " 2>/dev/null || echo '0')
@@ -1514,7 +1520,7 @@ council_heldout_gate() {
     # contain ':' or '|'); they are read separately from the held-out JSON block
     # below in the BLOCK branch.
     local gate_result
-    gate_result=$(_RESULTS_FILE="$results_file" _HELDOUT_FILE="$heldout_file" _WAIVERS_FILE="$waivers_file" python3 -c "
+    gate_result=$(_RESULTS_FILE="$results_file" _HELDOUT_FILE="$heldout_file" _WAIVERS_FILE="$waivers_file" python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, sys, os
 
 results_file = os.environ['_RESULTS_FILE']
@@ -1634,7 +1640,7 @@ print('%s %d %d' % (verdict, passed, failed))
     if [ "$verdict" = "BLOCK" ]; then
         # Read failing held-out titles directly from the data (colon/pipe-safe).
         local titles_json titles_display
-        titles_json=$(_RESULTS_FILE="$results_file" _HELDOUT_FILE="$heldout_file" _WAIVERS_FILE="$waivers_file" python3 -c "
+        titles_json=$(_RESULTS_FILE="$results_file" _HELDOUT_FILE="$heldout_file" _WAIVERS_FILE="$waivers_file" python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, os
 results = json.load(open(os.environ['_RESULTS_FILE']))
 heldout_ids = set(json.load(open(os.environ['_HELDOUT_FILE'])).get('held_out', []))
@@ -1653,7 +1659,7 @@ for cat in results.get('categories', []):
             titles.append(item.get('title', iid))
 print(json.dumps(titles[:5]))
 " 2>/dev/null || echo '[]')
-        titles_display=$(_T="$titles_json" python3 -c "
+        titles_display=$(_T="$titles_json" python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, os
 try:
     print(', '.join(json.loads(os.environ['_T'])))
@@ -1927,7 +1933,8 @@ council_evidence_gate() {
     local test_inconclusive_reason=""
     if [ -f "$tr_file" ]; then
         local test_status
-        test_status=$(_TR_FILE="$tr_file" python3 <<'PYEOF' 2>/dev/null || echo "INCONCLUSIVE:none:true"
+        test_status=$(_TR_FILE="$tr_file" python3 -E -s - <<'PYEOF' 2>/dev/null || echo "INCONCLUSIVE:none:true"
+import sys; sys.path[:] = [p for p in sys.path if p not in ("", ".")]
 import json, os, sys
 tr_file = os.environ['_TR_FILE']
 try:
@@ -1954,7 +1961,10 @@ if runner == 'none':
 elif passed is False:
     print('FAIL:%s:false' % runner)
 elif status == 'no_tests_run' or passed is not True:
-    print('INCONCLUSIVE:%s:true' % runner)
+    # Both are INCONCLUSIVE; NO_PASS names the second: no boolean pass was
+    # recorded at all (missing, null, or a non-boolean value), which is not a
+    # zero-test run.
+    print('%s:%s:true' % ('INCONCLUSIVE' if status == 'no_tests_run' else 'NO_PASS', runner))
 else:
     print('PASS:%s:true' % runner)
 PYEOF
@@ -1985,6 +1995,13 @@ PYEOF
             test_inconclusive="true"
             test_inconclusive_reason="no_tests_executed"
         fi
+        # A real runner label but no boolean pass recorded: the same
+        # pass-through INCONCLUSIVE, named for what it is. Not gated by the
+        # opt-out either: an unrecorded outcome is never affirmative.
+        if [ "$_verdict" = "NO_PASS" ]; then
+            test_inconclusive="true"
+            test_inconclusive_reason="no_pass_recorded"
+        fi
     else
         # Missing test-results.json: no suite was recorded at all. Like the
         # runner=="none" case this is not affirmative evidence, so classify it
@@ -2175,7 +2192,8 @@ DETAILS_EOF
         boot_inconclusive_reason="no_app_runner"
     elif command -v python3 >/dev/null 2>&1; then
         local _boot_status
-        _boot_status=$(_HEALTH="$_health_file" _STATE="$_state_file" python3 <<'PYEOF' 2>/dev/null || echo "INCONCLUSIVE:parse_error"
+        _boot_status=$(_HEALTH="$_health_file" _STATE="$_state_file" python3 -E -s - <<'PYEOF' 2>/dev/null || echo "INCONCLUSIVE:parse_error"
+import sys; sys.path[:] = [p for p in sys.path if p not in ("", ".")]
 import json, os
 health_file = os.environ.get('_HEALTH', '')
 state_file = os.environ.get('_STATE', '')
@@ -2338,7 +2356,8 @@ PYEOF
         persist_inconclusive="true"; persist_inconclusive_reason="not_serveable"
     elif command -v python3 >/dev/null 2>&1; then
         local _p_status
-        _p_status=$(_PF="$_proof_file" _ITER="${ITERATION_COUNT:-0}" python3 <<'PYEOF' 2>/dev/null || echo "MISSING"
+        _p_status=$(_PF="$_proof_file" _ITER="${ITERATION_COUNT:-0}" python3 -E -s - <<'PYEOF' 2>/dev/null || echo "MISSING"
+import sys; sys.path[:] = [p for p in sys.path if p not in ("", ".")]
 import json, os
 p = os.environ['_PF']
 if not os.path.isfile(p):
@@ -2401,7 +2420,8 @@ PYEOF
         auth_inconclusive="true"; auth_inconclusive_reason="not_serveable"
     elif command -v python3 >/dev/null 2>&1; then
         local _a_status
-        _a_status=$(_PF="$_proof_file" _STRICT="${LOKI_PROOF_AUTH_STRICT:-1}" _ITER="${ITERATION_COUNT:-0}" python3 <<'PYEOF' 2>/dev/null || echo "MISSING"
+        _a_status=$(_PF="$_proof_file" _STRICT="${LOKI_PROOF_AUTH_STRICT:-1}" _ITER="${ITERATION_COUNT:-0}" python3 -E -s - <<'PYEOF' 2>/dev/null || echo "MISSING"
+import sys; sys.path[:] = [p for p in sys.path if p not in ("", ".")]
 import json, os
 p = os.environ['_PF']
 strict = os.environ.get('_STRICT', '1') != '0'
@@ -2479,7 +2499,8 @@ PYEOF
         authz_inconclusive="true"; authz_inconclusive_reason="not_serveable"
     elif command -v python3 >/dev/null 2>&1; then
         local _authz_status
-        _authz_status=$(_PF="$_proof_file" _ITER="${ITERATION_COUNT:-0}" python3 <<'PYEOF' 2>/dev/null || echo "MISSING"
+        _authz_status=$(_PF="$_proof_file" _ITER="${ITERATION_COUNT:-0}" python3 -E -s - <<'PYEOF' 2>/dev/null || echo "MISSING"
+import sys; sys.path[:] = [p for p in sys.path if p not in ("", ".")]
 import json, os
 p = os.environ['_PF']
 if not os.path.isfile(p):
@@ -2736,7 +2757,7 @@ PYEOF
     local timestamp
     timestamp=$(date -u +"%Y-%m-%dT%H:%M:%SZ")
     local failures_json diff_ok tests_ok base_for_json
-    failures_json=$(_FAILURES="$failures" python3 -c "
+    failures_json=$(_FAILURES="$failures" python3 -E -s -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, os
 items = [s for s in os.environ['_FAILURES'].split('|') if s]
 print(json.dumps(items[:5]))
@@ -2753,11 +2774,11 @@ print(json.dumps(items[:5]))
     if [ "$authz_fails" = "true" ]; then authz_ok="false"; else authz_ok="true"; fi
     # Record WHY boot was inconclusive (no_app_runner / not_serveable / etc.) so a
     # consumer of the block report can tell a genuine boot pass from a pass-through.
-    boot_reason_json=$(_R="${boot_inconclusive_reason:-}" python3 -c "import json,os; print(json.dumps(os.environ['_R']))" 2>/dev/null || echo '""')
-    nomock_reason_json=$(_R="${nomock_inconclusive_reason:-}" python3 -c "import json,os; print(json.dumps(os.environ['_R']))" 2>/dev/null || echo '""')
-    persist_reason_json=$(_R="${persist_inconclusive_reason:-}" python3 -c "import json,os; print(json.dumps(os.environ['_R']))" 2>/dev/null || echo '""')
-    auth_reason_json=$(_R="${auth_inconclusive_reason:-}" python3 -c "import json,os; print(json.dumps(os.environ['_R']))" 2>/dev/null || echo '""')
-    authz_reason_json=$(_R="${authz_inconclusive_reason:-}" python3 -c "import json,os; print(json.dumps(os.environ['_R']))" 2>/dev/null || echo '""')
+    boot_reason_json=$(_R="${boot_inconclusive_reason:-}" python3 -E -s -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]; import json,os; print(json.dumps(os.environ['_R']))" 2>/dev/null || echo '""')
+    nomock_reason_json=$(_R="${nomock_inconclusive_reason:-}" python3 -E -s -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]; import json,os; print(json.dumps(os.environ['_R']))" 2>/dev/null || echo '""')
+    persist_reason_json=$(_R="${persist_inconclusive_reason:-}" python3 -E -s -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]; import json,os; print(json.dumps(os.environ['_R']))" 2>/dev/null || echo '""')
+    auth_reason_json=$(_R="${auth_inconclusive_reason:-}" python3 -E -s -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]; import json,os; print(json.dumps(os.environ['_R']))" 2>/dev/null || echo '""')
+    authz_reason_json=$(_R="${authz_inconclusive_reason:-}" python3 -E -s -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]; import json,os; print(json.dumps(os.environ['_R']))" 2>/dev/null || echo '""')
     base_for_json="${base_sha:-}"
     cat > "$ev_tmp" << EVIDENCE_EOF
 {
@@ -3395,7 +3416,7 @@ council_heuristic_review() {
             local _tr_file=".loki/quality/test-results.json"
             local _tests_ok=0
             if [ -f "$_tr_file" ] && command -v python3 >/dev/null 2>&1; then
-                _tests_ok=$(_TR="$_tr_file" python3 -c "
+                _tests_ok=$(_TR="$_tr_file" python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, os
 try:
     with open(os.environ['_TR']) as f:
@@ -3568,7 +3589,7 @@ council_evaluate_member() {
     local test_runner_seen="none"
     if [ -f "$tr_file" ]; then
         local _tr_status
-        _tr_status=$(_TR_FILE="$tr_file" python3 -c "
+        _tr_status=$(_TR_FILE="$tr_file" python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, os, sys
 try:
     with open(os.environ['_TR_FILE']) as f:
@@ -3625,7 +3646,7 @@ else:
             local _q _qcount
             for _q in pending in-progress blocked; do
                 [ -f "$loki_dir/queue/${_q}.json" ] || continue
-                _qcount=$(_QUEUE_FILE="$loki_dir/queue/${_q}.json" python3 -c "import json, os
+                _qcount=$(_QUEUE_FILE="$loki_dir/queue/${_q}.json" python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]; import json, os
 d = json.load(open(os.environ['_QUEUE_FILE']))
 print(len(d.get('tasks', d) if isinstance(d, dict) else d))" 2>/dev/null || echo "0")
                 # Guard against a non-numeric read (malformed file, python absent).
@@ -3762,7 +3783,7 @@ council_aggregate_votes() {
     # Serialize the votes array with json.dumps so backslashes/control chars are
     # escaped correctly (BUG fix: sed-only escaping produced invalid JSON).
     local votes_json
-    votes_json=$(_MEMBERS="$_members" _ROLES="$_roles" _VOTEVALS="$_vote_values" _REASONS="$_reasons" python3 -c "
+    votes_json=$(_MEMBERS="$_members" _ROLES="$_roles" _VOTEVALS="$_vote_values" _REASONS="$_reasons" python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, os
 def lines(name):
     v = os.environ.get(name, '')
@@ -3805,7 +3826,7 @@ print(json.dumps(out))
     _VERDICT="$verdict" \
     _VOTES="$votes_json" \
     _ROUND_FILE="$round_file" \
-    python3 -c "
+    python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, os
 from datetime import datetime, timezone
 round_data = {
@@ -3866,7 +3887,7 @@ council_devils_advocate_review() {
     local tr_file="$loki_dir/quality/test-results.json"
     if [ -f "$tr_file" ]; then
         local _tr_status
-        _tr_status=$(_TR_FILE="$tr_file" python3 -c "
+        _tr_status=$(_TR_FILE="$tr_file" python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, os, sys
 try:
     with open(os.environ['_TR_FILE']) as f:
@@ -3904,7 +3925,7 @@ else:
     # Skeptical check 2: Are there still failing tasks in the queue?
     if [ -f "$loki_dir/queue/failed.json" ]; then
         local failed_count
-        failed_count=$(_QUEUE_FILE="$loki_dir/queue/failed.json" python3 -c "import json, os; print(len(json.load(open(os.environ['_QUEUE_FILE']))))" 2>/dev/null || echo "0")
+        failed_count=$(_QUEUE_FILE="$loki_dir/queue/failed.json" python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]; import json, os; print(len(json.load(open(os.environ['_QUEUE_FILE']))))" 2>/dev/null || echo "0")
         if [ "$failed_count" -gt 0 ]; then
             ((issues_found++))
             issue_details="${issue_details}$failed_count tasks in failed queue; "
@@ -3950,7 +3971,7 @@ else:
     _ISSUES="$issues_found" \
     _DETAILS="${issue_details:-none}" \
     _DA_FILE="$da_file" \
-    python3 -c "
+    python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, os
 from datetime import datetime, timezone
 da_result = {
@@ -4046,7 +4067,7 @@ council_evaluate() {
             if loki_council_dispatch_agents "$ITERATION_COUNT" "${COUNCIL_PRD_PATH:-}"; then
                 local _va_round_file="$COUNCIL_STATE_DIR/votes/round-${ITERATION_COUNT}.json"
                 if [ -f "$_va_round_file" ]; then
-                    aggregate_result=$(_RF="$_va_round_file" python3 -c "import json, os; print(json.load(open(os.environ['_RF'])).get('verdict', 'CONTINUE'))" 2>/dev/null || echo "")
+                    aggregate_result=$(_RF="$_va_round_file" python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]; import json, os; print(json.load(open(os.environ['_RF'])).get('verdict', 'CONTINUE'))" 2>/dev/null || echo "")
                 fi
             fi
         fi
@@ -4068,7 +4089,7 @@ council_evaluate() {
         local complete_count=0
         local members_present=0
         if [ -f "$round_file" ]; then
-            complete_count=$(_RF="$round_file" python3 -c "import json, os; print(json.load(open(os.environ['_RF'])).get('complete_votes', 0))" 2>/dev/null || echo "0")
+            complete_count=$(_RF="$round_file" python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]; import json, os; print(json.load(open(os.environ['_RF'])).get('complete_votes', 0))" 2>/dev/null || echo "0")
             # WAVE13 CRITICAL quorum gate: how many voters actually responded
             # (total_members records the ACTUAL returned count -- see
             # voter-agents.sh). A degraded/partial dispatch response must never
@@ -4076,7 +4097,7 @@ council_evaluate() {
             # somehow read COMPLETE. This is defense-in-depth: the parser
             # already forces CONTINUE on undercount, but the completion-detection
             # trust core must independently assert full quorum before stopping.
-            members_present=$(_RF="$round_file" python3 -c "import json, os; print(json.load(open(os.environ['_RF'])).get('total_members', 0))" 2>/dev/null || echo "0")
+            members_present=$(_RF="$round_file" python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]; import json, os; print(json.load(open(os.environ['_RF'])).get('total_members', 0))" 2>/dev/null || echo "0")
         fi
         # Normalize to integers (guard against empty/non-numeric on read failure)
         case "$complete_count" in (''|*[!0-9]*) complete_count=0 ;; esac
@@ -4172,7 +4193,7 @@ council_managed_should_stop() {
     diff_summary=$(cd "$project_dir" 2>/dev/null && git diff --stat 2>/dev/null | tail -20 | tr '\n' ' ' || echo "")
     local test_summary=""
     if [ -f "$loki_dir/quality/test-results.json" ]; then
-        test_summary=$(_TRF="$loki_dir/quality/test-results.json" python3 -c "
+        test_summary=$(_TRF="$loki_dir/quality/test-results.json" python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, os
 try:
     d = json.load(open(os.environ['_TRF']))
@@ -4183,7 +4204,7 @@ except Exception:
     fi
     local pending_tasks="[]"
     if [ -f "$loki_dir/queue/pending.json" ]; then
-        pending_tasks=$(_QF="$loki_dir/queue/pending.json" python3 -c "
+        pending_tasks=$(_QF="$loki_dir/queue/pending.json" python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, os
 try:
     d = json.load(open(os.environ['_QF']))
@@ -4206,7 +4227,8 @@ except Exception:
     _CC_VERDICTS_DIR="$verdicts_dir" \
     _CC_LOKI_DIR="$loki_dir" \
     LOKI_TARGET_DIR="${TARGET_DIR:-$(pwd)}" \
-    python3 - <<'PYEOF' 2>/dev/null || exit_code=$?
+    python3 -E - <<'PYEOF' 2>/dev/null || exit_code=$?
+import sys; sys.path[:] = [p for p in sys.path if p not in ("", ".")]
 import json, os, sys, pathlib
 
 # Path setup: prefer project_dir so providers.managed resolves from main tree.
@@ -4383,7 +4405,7 @@ _council_convergence_evidence_green() {
     # file or runner=="none" (no suite) is NOT affirmative evidence -> not green.
     [ -f "$tr_file" ] || return 1
     local tr_state
-    tr_state=$(_TR_FILE="$tr_file" python3 -c "
+    tr_state=$(_TR_FILE="$tr_file" python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, os, sys
 try:
     with open(os.environ['_TR_FILE']) as f:
@@ -4406,7 +4428,7 @@ print('yes' if (runner != 'none' and passed is True
     local results_file="${TARGET_DIR:-.}/.loki/checklist/verification-results.json"
     if [ -f "$results_file" ]; then
         local cl_state
-        cl_state=$(_RESULTS_FILE="$results_file" python3 -c "
+        cl_state=$(_RESULTS_FILE="$results_file" python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, os, sys
 try:
     with open(os.environ['_RESULTS_FILE']) as f:
@@ -4655,7 +4677,7 @@ council_write_report() {
 REPORT_HEADER
 
     # Append vote history from state
-    _COUNCIL_STATE_FILE="$COUNCIL_STATE_DIR/state.json" python3 -c "
+    _COUNCIL_STATE_FILE="$COUNCIL_STATE_DIR/state.json" python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, os
 try:
     with open(os.environ['_COUNCIL_STATE_FILE']) as f:

package/autonomy/lib/workspace_diff.py

@@ -29,6 +29,21 @@ def _excluded(path):
     return path == ".loki" or path.startswith(".loki/")
 
 
+def _preexisting_untracked(repo_dir):
+    """Paths the user already had untracked when the Loki session branch was
+    minted (run.sh setup_agent_branch writes .loki/state/preexisting-untracked.z,
+    NUL-delimited, relative to the repo top). They are not this run's work, so
+    the receipt does not list them; tree_sha256 still binds their bytes. Returns
+    (prefix of repo_dir inside the repo, set of paths); empty when absent."""
+    try:
+        with open(os.path.join(repo_dir, ".loki", "state", "preexisting-untracked.z"), "rb") as fh:
+            raw = fh.read()
+    except OSError:
+        return "", frozenset()
+    paths = frozenset(p.decode("utf-8", "surrogateescape") for p in raw.split(b"\0") if p)
+    return (_git(repo_dir, ["rev-parse", "--show-prefix"]) or "").strip(), paths
+
+
 def _parse_numstat(raw):
     files = []
     for record in (raw or "").split("\0"):
@@ -107,7 +122,9 @@ def collect_workspace_diff(repo_dir, base, include_diffs=False):
                 diffs.append({"path": path, "patch": chunk})
 
     untracked = _git(repo_dir, ["ls-files", "--others", "--exclude-standard", "-z"])
-    for path in sorted(p for p in (untracked or "").split("\0") if p and not _excluded(p)):
+    prefix, preexisting = _preexisting_untracked(repo_dir)
+    for path in sorted(p for p in (untracked or "").split("\0")
+                       if p and not _excluded(p) and prefix + p not in preexisting):
         stat = _git(
             repo_dir,
             ["diff", "--no-index", "--no-renames", "--numstat", "-z", "--", "/dev/null", path],

package/autonomy/run.sh

@@ -2678,7 +2678,7 @@ _advance_current_phase() {
     [ -f "$orch" ] || return 0
     # Values are passed via argv (not interpolated into the source) so a phase or
     # path containing quotes can never break or inject into the python.
-    python3 -c "
+    python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, sys
 f, phase = sys.argv[1], sys.argv[2]
 try:
@@ -4377,7 +4377,7 @@ _loki_receipt_facts() {
     local pj="$loki_dir/proofs/$rid/proof.json"
     [ -f "$pj" ] || return 0
     local headline=""
-    headline="$(python3 -c "
+    headline="$(python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, sys
 try:
     d = json.load(open(sys.argv[1]))
@@ -4999,7 +4999,7 @@ except Exception:
     _LOKI_CS_ASSUMPTIONS_HIGH="$assumptions_high" \
     _LOKI_CS_OUT_FILE="$loki_dir/state/completion.json" \
     _LOKI_CS_LAST_ERROR="$loki_dir/state/LAST_ERROR.json" \
-    python3 -c "
+    python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, os, tempfile
 out = os.environ['_LOKI_CS_OUT_FILE']
 def i(v):
@@ -5219,7 +5219,7 @@ print_completion_card() {
     # split would collapse adjacent empties). Any failure leaves the card
     # unrendered. Trailing-newline guard: NUL-free, fields are single-line.
     local _fields
-    _fields="$(python3 -c "
+    _fields="$(python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json,sys
 try:
     d=json.load(open(sys.argv[1]))
@@ -5541,7 +5541,8 @@ validate_exec_manifest_result() {
     result_file=$(mktemp "${TARGET_DIR}/.loki/.exec-manifest-result.XXXXXX") || return 1
     LOKI_RESULT_FILE="$result_file" LOKI_RESULT_STREAM="$stream_name" \
       LOKI_RESULT_BASE="$base_sha" LOKI_RESULT_BRANCH="$branch" \
-      LOKI_RESULT_REPO="$TARGET_DIR" python3 <<'PY'
+      LOKI_RESULT_REPO="$TARGET_DIR" python3 -E - <<'PY'
+import sys; sys.path[:] = [p for p in sys.path if p not in ("", ".")]
 import json, os, subprocess
 paths = subprocess.check_output(
     ["git", "-C", os.environ["LOKI_RESULT_REPO"], "diff", "--name-only",
@@ -8098,7 +8099,7 @@ generate_proof_of_run() {
         ITERATION_COUNT="${ITERATION_COUNT:-0}" \
         PROVIDER_NAME="$provider" \
         PRD_PATH="${prd_path:-}" \
-        python3 "$gen" \
+        python3 -E "$gen" \
             --loki-dir "$loki_dir" \
             --loki-version "$ver" \
             --provider "$provider" \
@@ -8125,7 +8126,7 @@ generate_proof_of_run() {
     ITERATION_COUNT="${ITERATION_COUNT:-0}" \
     PROVIDER_NAME="$provider" \
     PRD_PATH="${prd_path:-}" \
-    python3 "$gen" \
+    python3 -E "$gen" \
         --loki-dir "$loki_dir" \
         --loki-version "$ver" \
         --provider "$provider" \
@@ -9132,6 +9133,21 @@ setup_agent_branch() {
 
     log_info "Branch protection enabled - creating agent branch: $branch_name (base: $cur)"
 
+    # Record the user's own untracked (not ignored) files, repo-wide,
+    # NUL-delimited and relative to the repo top, so commit_session_changes
+    # and the receipt (autonomy/lib/workspace_diff.py) leave them alone. Taken
+    # only when a branch is minted: on resume, untracked files can be the
+    # agent's own uncommitted work. .loki/ is self-ignored above.
+    local top="" snap=".loki/state/preexisting-untracked.z"
+    if top="$(git rev-parse --show-toplevel 2>/dev/null)" \
+       && git -C "$top" ls-files -z --others --exclude-standard > "$snap.tmp" 2>/dev/null \
+       && mv -f "$snap.tmp" "$snap" 2>/dev/null; then
+        :
+    else
+        rm -f "$snap.tmp" "$snap" 2>/dev/null
+        log_warn "Could not record pre-existing untracked files; the session commit may include them"
+    fi
+
     # Create and checkout the feature branch
     if ! git checkout -b "$branch_name" 2>/dev/null; then
         log_error "Failed to create agent branch: $branch_name"
@@ -9210,6 +9226,24 @@ commit_session_changes() {
         ':!*.key' ':!*.pem' ':!*.p12' ':!*.keystore' \
         ':!id_rsa*' ':!*.token' ':!credentials*' 2>/dev/null || true
 
+    # Unstage exactly the files that were untracked when the branch was minted
+    # (setup_agent_branch): they are the user's, not this session's work, and
+    # committing them here would delete them from disk on a later checkout of
+    # the base. Agent-created files stay staged. Skip an empty snapshot: an
+    # empty --pathspec-from-file resets the WHOLE index. No snapshot (older
+    # session): behave as before. If the unstage fails (git < 2.25), commit
+    # nothing rather than sweep the user's files in.
+    local preexisting="$PWD/.loki/state/preexisting-untracked.z" top=""
+    if [ -s "$preexisting" ]; then
+        if ! { top="$(git rev-parse --show-toplevel 2>/dev/null)" \
+               && git -C "$top" --literal-pathspecs reset -q \
+                      --pathspec-from-file="$preexisting" --pathspec-file-nul >/dev/null 2>&1; }; then
+            git reset -q >/dev/null 2>&1 || true
+            log_warn "Left uncommitted: could not exclude your pre-existing untracked files from the session commit (needs git 2.25+). Review and commit manually."
+            return 0
+        fi
+    fi
+
     # Nothing staged = clean no-op, never an error.
     if git diff --cached --quiet 2>/dev/null; then
         return 0
@@ -10227,7 +10261,8 @@ _loki_supervised_build_result_passes() {
     local result_file="$1"
     ! loki_is_supervised_simple_web && return 0
     [ -s "$result_file" ] || return 1
-    python3 - "$result_file" <<'PYEOF' 2>/dev/null
+    python3 -E - "$result_file" <<'PYEOF' 2>/dev/null
+import sys; sys.path[:] = [p for p in sys.path if p not in ("", ".")]
 import json
 import sys
 
@@ -10712,7 +10747,8 @@ SAEMPTYEOF
     # not product-specific copy or design opinions.
     local _ui_contract_out="" _ui_contract_rc=0
     _ui_contract_out=$(
-        _LOKI_CHANGED_FILES="$changed_files" python3 - "${TARGET_DIR:-.}" <<'PYEOF' 2>/dev/null
+        _LOKI_CHANGED_FILES="$changed_files" python3 -E - "${TARGET_DIR:-.}" <<'PYEOF' 2>/dev/null
+import sys; sys.path[:] = [p for p in sys.path if p not in ("", ".")]
 import os
 import re
 import sys
@@ -10778,8 +10814,14 @@ PYEOF
             [ -f "${TARGET_DIR:-.}/$f" ] || continue
             total_checked=$((total_checked + 1))
             local _py_compile_rc=0
+            # Same check as `python3 -m py_compile` (importlib's source_to_code
+            # is compile(bytes, path, "exec", dont_inherit=True)), but it
+            # writes no __pycache__/*.pyc into the user's repo, where the
+            # session commit would pick it up. -E and the sys.path filter
+            # (D7): the repo under check must not supply modules to the gate.
             LOKI_DEADLINE_IDLE_TIMEOUT=0 _loki_with_deadline "$gate_timeout" \
-                python3 -m py_compile "${TARGET_DIR:-.}/$f" 2>&1 || _py_compile_rc=$?
+                python3 -E -c 'import sys; sys.path[:] = [p for p in sys.path if p not in ("", ".")]; compile(open(sys.argv[1], "rb").read(), sys.argv[1], "exec", dont_inherit=True)' \
+                "${TARGET_DIR:-.}/$f" 2>&1 || _py_compile_rc=$?
             if [ "$_py_compile_rc" -ne 0 ]; then
                 findings=$((findings + 1))
                 if [ "$_py_compile_rc" -eq 124 ]; then
@@ -11096,7 +11138,7 @@ SECEMPTY
 
     # Run the scanner. exit 0 = no findings, 1 = findings, 2 = bad input.
     local raw rc=0
-    raw=$(python3 "$scanner" "${TARGET_DIR:-.}" --json 2>/dev/null) || rc=$?
+    raw=$(python3 -E "$scanner" "${TARGET_DIR:-.}" --json 2>/dev/null) || rc=$?
     if [ "$rc" -eq 2 ] || [ -z "$raw" ]; then
         cat > "$out_file" << 'SECEMPTY'
 {"rules_version":null,"findings":[],"summary":{"total":0,"by_severity":{}},"skipped":"scanner-error"}
@@ -11110,7 +11152,7 @@ SECEMPTY
     # It prints a final line: ACTIVE_HIGH=<n>\tACTIVE_TOTAL=<n>\tWAIVED=<n>
     # and writes the enriched receipt (findings carry a "waived" bool).
     local verdict
-    verdict=$(_SEC_RAW="$raw" _SEC_WAIVERS="$waivers_file" _SEC_OUT="$out_file" python3 -c '
+    verdict=$(_SEC_RAW="$raw" _SEC_WAIVERS="$waivers_file" _SEC_OUT="$out_file" python3 -E -c 'import sys; sys.path[:] = [p for p in sys.path if p not in ("", ".")]
 import json, os, sys
 raw = os.environ.get("_SEC_RAW", "")
 waivers_file = os.environ.get("_SEC_WAIVERS", "")
@@ -11610,7 +11652,7 @@ measure_test_coverage() {
                   --coverage.reportsDirectory=.loki/quality/vitest-cov >/dev/null 2>&1) || true
             local f="$target_dir/.loki/quality/vitest-cov/coverage-summary.json"
             if [ -f "$f" ]; then
-                COVERAGE_PCT=$(_LOKI_COV_F="$f" python3 -c "
+                COVERAGE_PCT=$(_LOKI_COV_F="$f" python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, os, sys
 try:
     d=json.load(open(os.environ['_LOKI_COV_F']))
@@ -11629,7 +11671,7 @@ except Exception:
                   --coverageDirectory=.loki/quality/jest-cov --passWithNoTests >/dev/null 2>&1) || true
             local f="$target_dir/.loki/quality/jest-cov/coverage-summary.json"
             if [ -f "$f" ]; then
-                COVERAGE_PCT=$(_LOKI_COV_F="$f" python3 -c "
+                COVERAGE_PCT=$(_LOKI_COV_F="$f" python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, os, sys
 try:
     d=json.load(open(os.environ['_LOKI_COV_F']))
@@ -11649,7 +11691,7 @@ except Exception:
                 _loki_run_pytest_with_timeout "$target_dir" \
                     --cov --cov-report="json:$pyc_json" -q >/dev/null 2>&1 || true
                 if [ -f "$pyc_json" ]; then
-                    COVERAGE_PCT=$(_LOKI_COV_F="$pyc_json" python3 -c "
+                    COVERAGE_PCT=$(_LOKI_COV_F="$pyc_json" python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, os, sys
 try:
     d=json.load(open(os.environ['_LOKI_COV_F']))
@@ -11689,7 +11731,7 @@ except Exception:
                 local out
                 out=$(cd "$target_dir" && timeout "$gate_timeout" cargo llvm-cov --json 2>/dev/null) || true
                 if [ -n "$out" ]; then
-                    COVERAGE_PCT=$(_LOKI_COV_JSON="$out" python3 -c "
+                    COVERAGE_PCT=$(_LOKI_COV_JSON="$out" python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, os, sys
 try:
     d=json.loads(os.environ['_LOKI_COV_JSON'])
@@ -12412,7 +12454,7 @@ TREOF
         local cov_below=false
         if [ "$COVERAGE_MEASURED" = "true" ] && [ -n "$COVERAGE_PCT" ]; then
             # Float-safe compare via python3 (pct may be e.g. 87.5).
-            if _LOKI_COV_PCT="$COVERAGE_PCT" _LOKI_COV_MIN="$min_coverage" python3 -c "
+            if _LOKI_COV_PCT="$COVERAGE_PCT" _LOKI_COV_MIN="$min_coverage" python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import os, sys
 try:
     pct=float(os.environ['_LOKI_COV_PCT']); mn=float(os.environ['_LOKI_COV_MIN'])
@@ -12437,7 +12479,7 @@ sys.exit(0 if pct < mn else 1)
         _LOKI_COV_BLOCKED="$coverage_block" \
         _LOKI_COV_RUNNER="$test_runner" \
         _LOKI_COV_OUT="$quality_dir/coverage.json" \
-        python3 -c "
+        python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, os, tempfile
 out=os.environ['_LOKI_COV_OUT']
 measured = os.environ.get('_LOKI_COV_MEASURED','false') == 'true'
@@ -12498,7 +12540,7 @@ os.replace(tmp, out)
         _LOKI_COV_BLOCKED="false" \
         _LOKI_COV_RUNNER="$test_runner" \
         _LOKI_COV_OUT="$quality_dir/coverage.json" \
-        python3 -c "
+        python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]
 import json, os, tempfile
 out=os.environ['_LOKI_COV_OUT']
 measured = os.environ.get('_LOKI_COV_MEASURED','false') == 'true'
@@ -12767,7 +12809,7 @@ run_doc_quality_gate() {
     local manifest="$project_dir/.loki/docs/docs-manifest.json"
     if [ -f "$manifest" ]; then
         local doc_sha
-        doc_sha=$(python3 -c "import json; print(json.load(open('$manifest')).get('git_sha', ''))" 2>/dev/null)
+        doc_sha=$(python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]; import json; print(json.load(open('$manifest')).get('git_sha', ''))" 2>/dev/null)
         if [ -n "$doc_sha" ]; then
             local behind
             behind=$(git -C "$project_dir" rev-list --count "$doc_sha..HEAD" 2>/dev/null || echo "0")
@@ -13198,7 +13240,7 @@ enforce_lsp_diagnostics() {
     fi
 
     if [ -f "$lsp_file" ]; then
-        verdict=$(_LOKI_LSP_FILE="$lsp_file" python3 -c '
+        verdict=$(_LOKI_LSP_FILE="$lsp_file" python3 -E -c 'import sys; sys.path[:] = [p for p in sys.path if p not in ("", ".")]
 import json, os, sys
 try:
     with open(os.environ["_LOKI_LSP_FILE"], encoding="utf-8") as handle:
@@ -13537,7 +13579,8 @@ council_verdicts_to_txt_files() {
     local out_dir_env="$review_dir"
     export LOKI_COUNCIL_OUT_DIR="$out_dir_env"
     export LOKI_COUNCIL_VERDICTS_JSON="$verdicts_json"
-    python3 << 'COUNCIL_WRITE'
+    python3 -E - << 'COUNCIL_WRITE'
+import sys; sys.path[:] = [p for p in sys.path if p not in ("", ".")]
 import json
 import os
 import re
@@ -13626,6 +13669,9 @@ _run_managed_review_council() {
 
     local result_json
     result_json=$(python3 << 'MANAGED_REVIEW' 2>&1
+# Drops the cwd (the agent's repo) from sys.path. No -E here: the
+# LOKI_MANAGED_REVIEW_FAKE_MODULE test hook below is found through PYTHONPATH.
+import sys; sys.path[:] = [p for p in sys.path if p not in ("", ".")]
 import json
 import os
 import sys
@@ -13724,7 +13770,7 @@ MANAGED_REVIEW
     fi
 
     local status
-    status=$(printf '%s' "$result_json" | python3 -c "import json,sys; d=json.loads(sys.stdin.read() or '{}'); print(d.get('status',''))" 2>/dev/null || echo "")
+    status=$(printf '%s' "$result_json" | python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]; import json,sys; d=json.loads(sys.stdin.read() or '{}'); print(d.get('status',''))" 2>/dev/null || echo "")
 
     if [ "$status" != "ok" ]; then
         local reason
@@ -16384,7 +16430,8 @@ REVIEW_WAVE_TIMING
     export LOKI_REVIEW_AGG_QSCORE="$quality_score"
     export LOKI_REVIEW_AGG_QMED="$nonblocking_medium"
     export LOKI_REVIEW_AGG_QLOW="$nonblocking_low"
-    python3 << 'AGG_SCRIPT'
+    python3 -E - << 'AGG_SCRIPT'
+import sys; sys.path[:] = [p for p in sys.path if p not in ("", ".")]
 import json, os
 result = {
     "review_id": os.environ["LOKI_REVIEW_AGG_ID"],
@@ -16527,7 +16574,8 @@ AGG_SCRIPT
 
         _LOKI_DA_AGG_FILE="$review_dir/$review_id/aggregate.json" \
             _LOKI_DA_STATUS="$da_status" _LOKI_DA_RC="$da_dispatch_rc" \
-            _LOKI_DA_SPECULATIVE="$da_speculative" python3 <<'DA_AGG_PATCH' 2>/dev/null || true
+            _LOKI_DA_SPECULATIVE="$da_speculative" python3 -E - <<'DA_AGG_PATCH' 2>/dev/null || true
+import sys; sys.path[:] = [p for p in sys.path if p not in ("", ".")]
 import json
 import os
 
@@ -17895,7 +17943,7 @@ is_completed() {
     # Check orchestrator state
     if [ -f ".loki/state/orchestrator.json" ]; then
         if command -v python3 &> /dev/null; then
-            local phase=$(python3 -c "import json; print(json.load(open('.loki/state/orchestrator.json')).get('currentPhase', ''))" 2>/dev/null || echo "")
+            local phase=$(python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]; import json; print(json.load(open('.loki/state/orchestrator.json')).get('currentPhase', ''))" 2>/dev/null || echo "")
             # Accept various completion states
             if [ "$phase" = "COMPLETED" ] || [ "$phase" = "complete" ] || [ "$phase" = "finalized" ] || [ "$phase" = "growth-loop" ]; then
                 return 0
@@ -21909,7 +21957,8 @@ _loki_supervised_completion_gates_pass() {
     local test_iteration="$quality_dir/.test-results.iter"
     if [ ! -s "$test_results" ] || [ ! -s "$test_iteration" ] \
        || [ "$(tr -d '[:space:]' < "$test_iteration" 2>/dev/null)" != "${ITERATION_COUNT:-0}" ] \
-       || ! python3 - "$test_results" <<'PYEOF' 2>/dev/null
+       || ! python3 -E - "$test_results" <<'PYEOF' 2>/dev/null
+import sys; sys.path[:] = [p for p in sys.path if p not in ("", ".")]
 import json
 import sys
 
@@ -27102,7 +27151,7 @@ main() {
     local _terminal_status=""
     local _terminal_state_file
     _terminal_state_file="$(_loki_state_file)"
-    _terminal_status=$(LOKI_STATE_FILE="$_terminal_state_file" python3 -c "import json, os; print(json.load(open(os.environ['LOKI_STATE_FILE'])).get('status',''))" 2>/dev/null || true)
+    _terminal_status=$(LOKI_STATE_FILE="$_terminal_state_file" python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]; import json, os; print(json.load(open(os.environ['LOKI_STATE_FILE'])).get('status',''))" 2>/dev/null || true)
     case "$_terminal_status" in
         deterministic_gates_passed|council_approved|council_force_approved|completion_promise_fulfilled|reuse_already_satisfied)
             if [ "$result" = "0" ]; then
@@ -27163,7 +27212,7 @@ main() {
     # Refresh its durable files against the final HEAD without notifying twice.
     local _completion_file="${TARGET_DIR:-.}/.loki/state/completion.json"
     local _completion_outcome=""
-    _completion_outcome=$(LOKI_COMPLETION_FILE="$_completion_file" python3 -c '
+    _completion_outcome=$(LOKI_COMPLETION_FILE="$_completion_file" python3 -E -c 'import sys; sys.path[:] = [p for p in sys.path if p not in ("", ".")]
 import json, os
 try:
     value = json.load(open(os.environ["LOKI_COMPLETION_FILE"], encoding="utf-8")).get("outcome", "")
@@ -27288,7 +27337,7 @@ except Exception:
     if [ "${LOKI_DURABLE_STATE:-0}" = "1" ]; then
         local _final_status _final_state_file
         _final_state_file="$(_loki_state_file)"
-        _final_status=$(LOKI_STATE_FILE="$_final_state_file" python3 -c "import json, os; print(json.load(open(os.environ['LOKI_STATE_FILE'])).get('status','unknown'))" 2>/dev/null || echo "unknown")
+        _final_status=$(LOKI_STATE_FILE="$_final_state_file" python3 -E -c "import sys; sys.path[:] = [p for p in sys.path if p not in ('', '.')]; import json, os; print(json.load(open(os.environ['LOKI_STATE_FILE'])).get('status','unknown'))" 2>/dev/null || echo "unknown")
         case "$_final_status" in
             council_approved|council_force_approved|deterministic_gates_passed|completion_promise_fulfilled|paused|interrupted|stopped)
                 result=0 ;;

package/dashboard/__init__.py

@@ -7,7 +7,7 @@ Modules:
     control: Session control API (start/stop/pause/resume)
 """
 
-__version__ = "9.52.0"
+__version__ = "9.53.0"
 
 # Expose the control app for easy import
 try:

package/docs/INSTALLATION.md

@@ -2,7 +2,7 @@
 
 The flagship product of [Autonomi](https://www.autonomi.dev/). Loki Mode is a spec-driven autonomous builder with a built-in trust layer that takes any spec to a deployed product and verifies completion with evidence (quality gates plus a completion council), not just a "done" claim. Complete installation instructions for all platforms and use cases.
 
-**Version:** v9.52.0
+**Version:** v9.53.0
 
 ---
 

package/docs/v10/BACKLOG.md

@@ -80,6 +80,16 @@ Status values: todo, in progress, shipped (version), parked (reason).
 51. **With `-E`, cryptography supplied via `PYTHONPATH`/`PYTHONUSERBASE` reads NOT CHECKED**; say so in the NOT CHECKED message.
 52. **CI check name:** "Moat suite" shows green at 0 of 9; consider a name that says "no rule failed" so the check mark is not read as "moat proven" (the step summary already carries the count).
 
+53. **Checklist verification still imports from the agent repo:** `autonomy/prd-checklist.sh` (a script call near 994 and about 9 inline `python3 -c` sites) is outside the cycle-2 fix; apply D7 there next (cycle-2 slice S).
+54. **Council helpers still unguarded:** `autonomy/lib/voter-agents.sh` (3 sites parse voter output), `autonomy/council-v2.sh` (7), `autonomy/lib/done-recognition.sh` (16), `autonomy/lib/proof-check.sh` (3); about 217 non-verdict inline sites in `run.sh`; script-form calls (claim_grounding, requirements helper, deadline.py) inherit `PYTHONPATH`. Managed council inserts `PROJECT_DIR or os.getcwd()` on `sys.path` behind experimental flags.
+55. **Zero-test honesty on bash:** `enforce_test_coverage`'s #82 zero-test branch downgrades only the JSON record; `test_passed` stays true, so `run.sh` (~12533) still touches `quality/unit-tests.pass` and logs "passed". `evidence-gate-details.json` records `tests.pass: true` for every inconclusive outcome.
+56. **Bun npm-test fallback has no zero-test detection**, and the Bun reader uses `passed`/`failed` while the bash writer emits `passed_count`/`failed_count` (the detail shows an unmeasured failed=0).
+
+57. **Resume must re-snapshot untracked files (data risk).** The snapshot is taken only when a session branch is minted; on the resume and already-on-loki paths (`run.sh` ~9100-9119) a file the user created between sessions is swept into the commit and removed from disk on checkout of the base. Add the current untracked list to the snapshot on both reuse paths (cycle-2 council).
+58. **Gitignored user files are swept when the agent rewrites `.gitignore` (data risk).** Also snapshot `git ls-files -z --others --ignored --exclude-standard --directory` and prefix-match directory entries in `workspace_diff` (cycle-2 council).
+59. **Agent edits to pre-existing untracked files are omitted from the receipt (new in v9.53.0).** Store a blob hash per snapshot entry; list a path whose hash changed (for example `preexisting_modified`) while still never committing the user's file (cycle-2 council). Not a false pass: no verdict reads the list.
+60. **Bun `runTestCoverage` accepts a stale `test-results.json`** (no freshness check against `.loki/quality/.test-results.iter`), and an inconclusive coverage still lands in `GateOutcome.passed[]` with an "(gate did not run)" log line.
+
 ## Later milestones
 
 M1 one command, M2 Seal and Wall, M3 assign like a teammate, M4 system map, M5 the line, M6 ship and operate, M7 one screen, M8 legacy lane, M9 enterprise readiness, M10 simplify and ship v10.0.0. Items get broken out here when their milestone comes up.

package/docs/v10/METRICS.md

@@ -42,5 +42,6 @@ produced it. "Not measured" is a real value here: nothing is estimated.
 
 | Property | Status | Command |
 |---|---|---|
-| all 9 | 0 of 9 proven; 45 cases, 21 pass, 24 pending with milestones (2026-09-25, v9.52.0, macOS and ubuntu CI) | `bash tests/moat/run.sh` |
+| all 9 | 1 of 9 proven (P6); 48 cases, 25 pass, 23 pending with milestones (2026-09-26, v9.53.0) | `bash tests/moat/run.sh` |
+| history | v9.52.0: 0 of 9, 45 cases, 21 pass, 24 pending | - |
 | runtime | about 15s locally (9 scripts in parallel), about 1m15s CI job | `time bash tests/moat/run.sh` |

package/docs/v10/PROGRESS.md

@@ -23,13 +23,27 @@
 - Council rounds 4-8 each found one more real verifier hole, all fixed with red-then-green tests: `--help` skipped the check (rounds 4-5: verify now never exits 0 without a verdict); the checkout could supply the verifier's Python modules through `python3 -` (round 6), through `PYTHONPATH`/`sitecustomize.py` (round 7: `python3 -E`, D7), and through chain stage subprocesses (round 8).
 - Council round 9: **3 of 3 APPROVE** at `5119f897`. One unreproduced observation (P1.modified-field-fails failed once in 7 local runs; 60 further runs under load passed).
 - Release v9.52.0 cut: version bump, CHANGELOG, dashboard rebuild (no diff), dist rebuild, tarball smoke-tested from a fresh PATH.
+- **v9.52.0 verified on all channels (2026-09-26):** Release run green (required-ci: Tests, Bun Parity, Security Audit at `7c280ead`); npm `latest` 9.52.0 with `gitHead` `7c280ead`; tag `v9.52.0^{}` = `7c280ead`; GitHub release published; Docker Hub `9.52.0` amd64 + arm64; Homebrew formula sha256 equals the downloaded release tarball. Published package smoke-tested on both routes from a fresh PATH (reports 9.52.0; `verify -h` 64). Validation PR #216 auto-merged by GitHub; its branch is gone.
 
 ## Shipped in v10 program
 
+- **v9.53.0** (2026-09-26): P6 in-place brownfield proven (moat 1 of 9); user untracked files never swept into session commits; no bytecode from the syntax gate; Bun gate never passes an inconclusive result; council and runner verdict paths cannot import from the agent repo.
 - **v9.52.0** (2026-09-25): moat suite `tests/moat/` (45 cases, 0 of 9 properties proven, 24 pending with milestones, ratchet baseline set by this release); verifier fixes (Bun `--jwks`, stripped signature, malformed tokens, strict flags and help, `python3 -E` on every verify path, exit contract 64/66); council `pass` readers fail closed; honest `doctor --airgap`; main-red fix.
 
-## Next
+### Cycle 2 (2026-09-26)
 
-1. Verify v9.52.0 on npm, Docker, Homebrew and the GitHub release; close validation PR #216.
-2. BACKLOG 15 (untracked files swept into the session commit: data risk), 37 (Bun passes an inconclusive test result) and 43 (inline Python on council verdict paths importable from the agent repo): honest-verdict and data-risk items first.
-3. Then P7 (no fabricated data) and P9 (Rule of Two), the moat gaps with the smallest fix, and M0 measurement (catalog + seeded-defect corpus).
+- Dev fleet (3 worktree slices): untracked-file sweep and bytecode (BACKLOG 15, 16), Bun inconclusive pass and council reason naming (37, 38), cwd shadowing on council and runner verdict paths (43). Integrated plus the D7 guard on the new syntax check.
+- Moat: **1 of 9 proven** (P6); ratchet live against v9.52.0 (23 pending, 48 registered).
+- Council: 3 of 3 APPROVE on the first round. Non-blocking data-safety findings recorded as BACKLOG 57-60.
+- Released as v9.53.0.
+
+## Next (after cycle 2)
+
+1. Brownfield data safety: BACKLOG 57, 58, 59 (resume re-snapshot, gitignored files, receipt omission).
+2. Honest verdict: BACKLOG 53-56, 60 (checklist verification and council helpers under D7; zero-test record; stale results).
+3. Then P7 (no fabricated data), P9 (Rule of Two), M0 measurement.
+
+## Next (before cycle 2, kept for history)
+
+1. Cycle 2: BACKLOG 15 (untracked files swept into the session commit: data risk), 37 (Bun passes an inconclusive test result) and 43 (inline Python on council verdict paths importable from the agent repo): honest-verdict and data-risk items first.
+2. Then P7 (no fabricated data) and P9 (Rule of Two), the moat gaps with the smallest fix, and M0 measurement (catalog + seeded-defect corpus).

package/loki-ts/dist/loki.js

@@ -1,5 +1,5 @@
 // @bun
-var mt=Object.create;var{getPrototypeOf:ut,defineProperty:jG,getOwnPropertyNames:dt}=Object;var pt=Object.prototype.hasOwnProperty;function ct($){return this[$]}var lt,it,at=($,X,Q)=>{var z=$!=null&&typeof $==="object";if(z){var Z=X?lt??=new WeakMap:it??=new WeakMap,K=Z.get($);if(K)return K}Q=$!=null?mt(ut($)):{};let J=X||!$||!$.__esModule?jG(Q,"default",{value:$,enumerable:!0}):Q;for(let q of dt($))if(!pt.call(J,q))jG(J,q,{get:ct.bind($,q),enumerable:!0});if(z)Z.set($,J);return J};var zq=($,X)=>()=>(X||$((X={exports:{}}).exports,X),X.exports);var ot=($)=>$;function st($,X){this[$]=ot.bind(null,X)}var B1=($,X)=>{for(var Q in X)jG($,Q,{get:X[Q],enumerable:!0,configurable:!0,set:st.bind(X,Q)})};var s=($,X)=>()=>($&&(X=$($=0)),X);var w5=import.meta.require;var WR={};B1(WR,{lokiDir:()=>h0,homeLokiDir:()=>GQ,findRepoRootForVersion:()=>AG,REPO_ROOT:()=>L1});import{resolve as h2,dirname as LG}from"path";import{fileURLToPath as nt}from"url";import{existsSync as Zq}from"fs";import{homedir as rt}from"os";function tt(){let $=HR;for(let X=0;X<6;X++){if(Zq(h2($,"VERSION"))&&Zq(h2($,"autonomy/run.sh")))return $;let Q=LG($);if(Q===$)break;$=Q}return h2(HR,"..","..","..")}function AG($){let X=$;for(let Q=0;Q<6;Q++){if(Zq(h2(X,"VERSION"))&&Zq(h2(X,"autonomy/run.sh")))return X;let z=LG(X);if(z===X)break;X=z}return h2($,"..","..","..")}function h0(){return process.env.LOKI_DIR??h2(process.cwd(),".loki")}function GQ(){return h2(rt(),".loki")}var HR,L1;var k1=s(()=>{HR=LG(nt(import.meta.url));L1=tt()});import{readFileSync as et}from"fs";import{resolve as $e,dirname as Xe}from"path";import{fileURLToPath as Qe}from"url";function j9(){if(n3!==null)return n3;let $="9.52.0";if(typeof $==="string"&&$.length>0)return n3=$,n3;try{let X=Xe(Qe(import.meta.url)),Q=AG(X);n3=et($e(Q,"VERSION"),"utf-8").trim()}catch{n3="unknown"}return n3}var n3=null;var Kq=s(()=>{k1()});var 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 `),process.stdout.write(`Install with:
 `),process.stdout.write(`  brew install jq    (macOS)
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set LOKI_GATE_SEMANTIC_TESTS_BLOCK=true to block)"}}if(q===124)return S2(KQ(Z)),{passed:!0,inconclusive:!0,detail:"semantic_tests: detector timed out -- inconclusive, not blocking"};let H=$q(V,/\[(MEDIUM|LOW)\]/);if(H.length>0)k2(KQ(Z),"# Semantic test advisory findings (MED/LOW, non-blocking)",H);else S2(KQ(Z));return{passed:!0,detail:`semantic_tests: no blocking findings (rc ${q})`}}async function Kt($){let Q=process.env.LOKI_STUB_GATE_INVARIANTS;if(Q==="fail"||Q==="pass")return X2("invariants");let z=$?.cwd??process.cwd(),Z=$?.lokiDir??h0(),K=process.env.LOKI_INVARIANT_DETECTOR??K1(L1,"tests","detect-invariant-violations.sh");if(!L5(K))return S2(JQ(Z)),{passed:!0,inconclusive:!0,detail:"invariants: detector not found -- gate did not run"};let J=300000,q,V;try{let W=await $1(["bash",K,"--strict"],{cwd:z,env:{LOKI_SCAN_DIR:z},timeoutMs:J});q=W.exitCode,V=`${W.stdout}${W.stderr}`}catch{return S2(JQ(Z)),{passed:!0,inconclusive:!0,detail:"invariants: detector spawn failed -- inconclusive, not blocking"}}let Y=process.env.LOKI_GATE_INVARIANTS_BLOCK,U=Y==="true"||Y==="1";if(q===1){if(k2(JQ(Z),"# Invariant findings (CRITICAL/HIGH block this completion)",$q(V,/\[(CRITICAL|HIGH|MEDIUM|LOW)\]/)),U)return{passed:!1,detail:"invariants: CRITICAL/HIGH invariant violation detected -- BLOCK (LOKI_GATE_INVARIANTS_BLOCK)"};return{passed:!0,detail:"invariants: CRITICAL/HIGH invariant violation detected -- advisory (surfaced; set LOKI_GATE_INVARIANTS_BLOCK=true to block)"}}if(q===124)return S2(JQ(Z)),{passed:!0,inconclusive:!0,detail:"invariants: detector timed out -- inconclusive, not blocking"};let H=$q(V,/\[(MEDIUM|LOW)\]/);if(H.length>0)k2(JQ(Z),"# Invariant advisory findings (MED/LOW, non-blocking)",H);else S2(JQ(Z));return{passed:!0,detail:`invariants: no blocking violations (rc ${q})`}}function qt($,X){if(process.env.LOKI_HEAL_MODE==="true"||process.env.LOKI_HEAL_MODE==="1")return!0;let Q=K1($,".loki","healing"),z=K1(Q,"friction-map.json");if(L5(z)){if(!X)return!0;try{let Z=T4(z,"utf8"),K=JSON.parse(Z),J=Array.isArray(K.entries)?K.entries:[],q=X.toLowerCase();for(let V of J){let Y=(V.file??"").toLowerCase().trim();if(Y&&q.includes(Y))return!0}return!1}catch{return!0}}return!1}function q31($){let X={};try{let Q=T4(K1($,".loki","agents","installed.json"),"utf8"),z=JSON.parse(Q),Z=Array.isArray(z)?z:z.agents??[],K=100;for(let J of Z){let q=(J?.type??"").trim();if(!q||q in Jt||q in X)continue;let V=(J.focus??[]).map((Y)=>String(Y).trim().toLowerCase()).filter((Y)=>Y.length>0);if(V.length===0)continue;X[q]={keywords:V,focus:J.capabilities||J.name||q,checks:`Review from ${J.name??q} perspective: ${(J.focus??[]).join(", ")}`,priority:K++}}}catch{}return X}function Y31($){let X=V31[($??"").trim().toLowerCase()]??2;return X<2?2:X}function Vt($,X,Q={}){let z=Q.healingActive===!0,Z={};for(let[M,A]of Object.entries(Jt)){if(M==="legacy-healing-auditor"&&!z)continue;Z[M]=A}let K=`${$} ${X}`.toLowerCase(),J={};for(let[M,A]of Object.entries(Z)){let j=0;for(let B of A.keywords)if(K.includes(B))j+=1;J[M]=j}let q=Y31(Q.complexity),V=Object.keys(Z).slice().sort((M,A)=>{let j=J[M]??0,B=J[A]??0;if(B!==j)return B-j;return Z[M].priority-Z[A].priority}),Y=Object.values(J).every((M)=>M===0),U;if(Y){U=["security-sentinel","test-coverage-auditor"];for(let M of V){if(U.length>=q)break;if(!U.includes(M))U.push(M)}U=U.slice(0,Math.max(q,2))}else U=V.slice(0,q);let H=2,W=Q.cwd===void 0?{}:q31(Q.cwd),G=[];for(let[M,A]of Object.entries(W)){let j=0;for(let B of A.keywords)if(K.includes(B))j+=1;J[M]=j}for(let M of Object.keys(W).sort((A,j)=>{let B=J[A]??0,L=J[j]??0;if(L!==B)return L-B;return W[A].priority-W[j].priority})){if(G.length>=H)break;if((J[M]??0)>0)G.push(M)}return{reviewers:[K31,J31,...U.map((M)=>{let A=Z[M];return{name:M,focus:A.focus,checks:A.checks}}),...G.map((M)=>{let A=W[M];return{name:M,focus:A.focus,checks:A.checks}})],scores:J,pool_size:Object.keys(Z).length+G.length}}function Yt($,X,Q){return`You are ${$.name}. Your SOLE focus is: ${$.focus}.
@@ -1344,4 +1344,4 @@ Set LOKI_LEGACY_BASH=1 to force the bash CLI for every command.
 `),2}case"start":{let{runStart:z}=await Promise.resolve().then(() => (vt(),_t));return z(Q)}default:return process.stderr.write(`Unknown command: ${X}
 `),process.stderr.write(ht),2}}ER();process.on("SIGINT",()=>process.exit(130));process.on("SIGTERM",()=>process.exit(143));var q61=await J61(Bun.argv.slice(2));process.exit(q61);
 
-//# debugId=A13974976FEDA6E710941BC9D02255FD
+//# debugId=09DC6EF45F50512C5ACB2713447872BB

package/mcp/__init__.py

@@ -75,4 +75,4 @@ try:
 except ImportError:
     __all__ = ['mcp']
 
-__version__ = '9.52.0'
+__version__ = '9.53.0'

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "loki-mode",
   "mcpName": "io.github.asklokesh/loki-mode",
-  "version": "9.52.0",
+  "version": "9.53.0",
   "description": "Loki Mode by Autonomi. Autonomous spec-to-product system: takes a PRD, GitHub issue, OpenAPI/JSON/YAML, or one-line brief to a deployed app via the RARV-C closure loop with 8 quality gates. Provider-agnostic (Claude Code, OpenAI Codex, Cline, Aider, opencode).",
   "keywords": [
     "agent",

package/plugins/loki-mode/.claude-plugin/plugin.json

@@ -2,7 +2,7 @@
   "$schema": "https://json.schemastore.org/claude-code-plugin-manifest.json",
   "name": "loki-mode",
   "displayName": "Loki Mode",
-  "version": "9.52.0",
+  "version": "9.53.0",
   "description": "Autonomous spec-to-product build system with a built-in trust layer (RARV-C closure loop, 8 quality gates, completion council). Ships Loki's spec-hardening, drift-detection, and deterministic PR verification commands plus the Loki MCP server.",
   "author": {
     "name": "Autonomi",