fix: eliminate shell injection vectors in deploy/research/state scripts

- lib-state.sh: all 7 functions now use os.environ instead of string interpolation
- deploy.sh: syntax checker uses sys.argv[1] instead of '$f' interpolation
- research-session.sh: per-command auth header instead of credential helper,
  tweet parsers use sys.argv instead of '$OUTFILE' interpolation
- state_end_session: now writes pr_number to session JSON via env var

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

ops/agent-state/lib-state.sh

@@ -14,15 +14,6 @@ _state_dir() {
     echo "$STATE_ROOT/$agent"
 }
 
-# Atomic write: write to tmp file, then rename. Prevents partial reads.
-_atomic_write() {
-    local filepath="$1"
-    local content="$2"
-    local tmpfile="${filepath}.tmp.$$"
-    echo "$content" > "$tmpfile"
-    mv -f "$tmpfile" "$filepath"
-}
-
 # --- Report (current status) ---
 
 state_read_report() {
@@ -37,17 +28,18 @@ state_update_report() {
     local summary="$3"
     local file="$(_state_dir "$agent")/report.json"
 
-    # Read existing, merge with updates using python (available on VPS)
+    _STATE_FILE="$file" _STATE_AGENT="$agent" _STATE_STATUS="$status" \
+    _STATE_SUMMARY="$summary" _STATE_TS="$(date -u +%Y-%m-%dT%H:%M:%SZ)" \
     python3 -c "
-import json, sys
+import json, os
 try:
-    with open('$file') as f:
+    with open(os.environ['_STATE_FILE']) as f:
         data = json.load(f)
 except:
-    data = {'agent': '$agent'}
-data['status'] = '$status'
-data['summary'] = '''$summary'''
-data['updated_at'] = '$(date -u +%Y-%m-%dT%H:%M:%SZ)'
+    data = {'agent': os.environ['_STATE_AGENT']}
+data['status'] = os.environ['_STATE_STATUS']
+data['summary'] = os.environ['_STATE_SUMMARY']
+data['updated_at'] = os.environ['_STATE_TS']
 print(json.dumps(data, indent=2))
 " | _atomic_write_stdin "$file"
 }
@@ -75,25 +67,35 @@ state_finalize_report() {
     local next_priority="${11:-null}"
     local file="$(_state_dir "$agent")/report.json"
 
+    _STATE_FILE="$file" _STATE_AGENT="$agent" _STATE_STATUS="$status" \
+    _STATE_SUMMARY="$summary" _STATE_SESSION_ID="$session_id" \
+    _STATE_STARTED="$started_at" _STATE_ENDED="$ended_at" \
+    _STATE_OUTCOME="$outcome" _STATE_SOURCES="$sources" \
+    _STATE_BRANCH="$branch" _STATE_PR="$pr_number" \
+    _STATE_NEXT="$next_priority" \
     python3 -c "
-import json
+import json, os
+e = os.environ
+sources = int(e['_STATE_SOURCES']) if e['_STATE_SOURCES'].isdigit() else 0
+pr = int(e['_STATE_PR']) if e['_STATE_PR'].isdigit() else None
+next_p = None if e['_STATE_NEXT'] == 'null' else e['_STATE_NEXT']
 data = {
-    'agent': '$agent',
-    'updated_at': '$ended_at',
-    'status': '$status',
-    'summary': '''$summary''',
+    'agent': e['_STATE_AGENT'],
+    'updated_at': e['_STATE_ENDED'],
+    'status': e['_STATE_STATUS'],
+    'summary': e['_STATE_SUMMARY'],
     'current_task': None,
     'last_session': {
-        'id': '$session_id',
-        'started_at': '$started_at',
-        'ended_at': '$ended_at',
-        'outcome': '$outcome',
-        'sources_archived': $sources,
-        'branch': '$branch',
-        'pr_number': $pr_number
+        'id': e['_STATE_SESSION_ID'],
+        'started_at': e['_STATE_STARTED'],
+        'ended_at': e['_STATE_ENDED'],
+        'outcome': e['_STATE_OUTCOME'],
+        'sources_archived': sources,
+        'branch': e['_STATE_BRANCH'],
+        'pr_number': pr
     },
     'blocked_by': None,
-    'next_priority': $([ "$next_priority" = "null" ] && echo "None" || echo "'$next_priority'")
+    'next_priority': next_p
 }
 print(json.dumps(data, indent=2))
 " | _atomic_write_stdin "$file"
@@ -113,19 +115,23 @@ state_start_session() {
     started_at="$(date -u +%Y-%m-%dT%H:%M:%SZ)"
     local file="$(_state_dir "$agent")/session.json"
 
+    _STATE_FILE="$file" _STATE_AGENT="$agent" _STATE_SID="$session_id" \
+    _STATE_STARTED="$started_at" _STATE_TYPE="$type" _STATE_DOMAIN="$domain" \
+    _STATE_BRANCH="$branch" _STATE_MODEL="$model" _STATE_TIMEOUT="$timeout" \
     python3 -c "
-import json
+import json, os
+e = os.environ
 data = {
-    'agent': '$agent',
-    'session_id': '$session_id',
-    'started_at': '$started_at',
+    'agent': e['_STATE_AGENT'],
+    'session_id': e['_STATE_SID'],
+    'started_at': e['_STATE_STARTED'],
     'ended_at': None,
-    'type': '$type',
-    'domain': '$domain',
-    'branch': '$branch',
+    'type': e['_STATE_TYPE'],
+    'domain': e['_STATE_DOMAIN'],
+    'branch': e['_STATE_BRANCH'],
     'status': 'running',
-    'model': '$model',
-    'timeout_seconds': $timeout,
+    'model': e['_STATE_MODEL'],
+    'timeout_seconds': int(e['_STATE_TIMEOUT']),
     'research_question': None,
     'belief_targeted': None,
     'disconfirmation_target': None,
@@ -149,13 +155,18 @@ state_end_session() {
     local pr_number="${4:-null}"
     local file="$(_state_dir "$agent")/session.json"
 
+    _STATE_FILE="$file" _STATE_OUTCOME="$outcome" _STATE_SOURCES="$sources" \
+    _STATE_PR="$pr_number" _STATE_TS="$(date -u +%Y-%m-%dT%H:%M:%SZ)" \
     python3 -c "
-import json
-with open('$file') as f:
+import json, os
+e = os.environ
+with open(e['_STATE_FILE']) as f:
     data = json.load(f)
-data['ended_at'] = '$(date -u +%Y-%m-%dT%H:%M:%SZ)'
-data['status'] = '$outcome'
-data['sources_archived'] = $sources
+data['ended_at'] = e['_STATE_TS']
+data['status'] = e['_STATE_OUTCOME']
+data['sources_archived'] = int(e['_STATE_SOURCES']) if e['_STATE_SOURCES'].isdigit() else 0
+pr = e.get('_STATE_PR', 'null')
+data['pr_number'] = int(pr) if pr.isdigit() else None
 print(json.dumps(data, indent=2))
 " | _atomic_write_stdin "$file"
 }
@@ -168,13 +179,17 @@ state_journal_append() {
     shift 2
     # Remaining args are key=value pairs for extra fields
     local file="$(_state_dir "$agent")/journal.jsonl"
-    local extras=""
-    for kv in "$@"; do
-        local key="${kv%%=*}"
-        local val="${kv#*=}"
-        extras="$extras, \"$key\": \"$val\""
-    done
-    echo "{\"ts\":\"$(date -u +%Y-%m-%dT%H:%M:%SZ)\",\"event\":\"$event\"$extras}" >> "$file"
+
+    _STATE_TS="$(date -u +%Y-%m-%dT%H:%M:%SZ)" _STATE_EVT="$event" \
+    python3 -c "
+import json, os, sys
+entry = {'ts': os.environ['_STATE_TS'], 'event': os.environ['_STATE_EVT']}
+for pair in sys.argv[1:]:
+    k, _, v = pair.partition('=')
+    if k:
+        entry[k] = v
+print(json.dumps(entry))
+" "$@" >> "$file"
 }
 
 # --- Metrics ---
@@ -185,25 +200,29 @@ state_update_metrics() {
     local sources="${3:-0}"
     local file="$(_state_dir "$agent")/metrics.json"
 
+    _STATE_FILE="$file" _STATE_AGENT="$agent" _STATE_OUTCOME="$outcome" \
+    _STATE_SOURCES="$sources" _STATE_TS="$(date -u +%Y-%m-%dT%H:%M:%SZ)" \
     python3 -c "
-import json
+import json, os
+e = os.environ
 try:
-    with open('$file') as f:
+    with open(e['_STATE_FILE']) as f:
         data = json.load(f)
 except:
-    data = {'agent': '$agent', 'lifetime': {}, 'rolling_30d': {}}
+    data = {'agent': e['_STATE_AGENT'], 'lifetime': {}, 'rolling_30d': {}}
 
 lt = data.setdefault('lifetime', {})
 lt['sessions_total'] = lt.get('sessions_total', 0) + 1
-if '$outcome' == 'completed':
+outcome = e['_STATE_OUTCOME']
+if outcome == 'completed':
     lt['sessions_completed'] = lt.get('sessions_completed', 0) + 1
-elif '$outcome' == 'timeout':
+elif outcome == 'timeout':
     lt['sessions_timeout'] = lt.get('sessions_timeout', 0) + 1
-elif '$outcome' == 'error':
+elif outcome == 'error':
     lt['sessions_error'] = lt.get('sessions_error', 0) + 1
-lt['sources_archived'] = lt.get('sources_archived', 0) + $sources
+lt['sources_archived'] = lt.get('sources_archived', 0) + (int(e['_STATE_SOURCES']) if e['_STATE_SOURCES'].isdigit() else 0)
 
-data['updated_at'] = '$(date -u +%Y-%m-%dT%H:%M:%SZ)'
+data['updated_at'] = e['_STATE_TS']
 print(json.dumps(data, indent=2))
 " | _atomic_write_stdin "$file"
 }
@@ -227,17 +246,21 @@ state_send_message() {
     local file="$inbox/${msg_id}.json"
 
     mkdir -p "$inbox"
+    _STATE_FILE="$file" _STATE_MSGID="$msg_id" _STATE_FROM="$from" \
+    _STATE_TO="$to" _STATE_TS="$(date -u +%Y-%m-%dT%H:%M:%SZ)" \
+    _STATE_TYPE="$type" _STATE_SUBJECT="$subject" _STATE_BODY="$body" \
     python3 -c "
-import json
+import json, os
+e = os.environ
 data = {
-    'id': '$msg_id',
-    'from': '$from',
-    'to': '$to',
-    'created_at': '$(date -u +%Y-%m-%dT%H:%M:%SZ)',
-    'type': '$type',
+    'id': e['_STATE_MSGID'],
+    'from': e['_STATE_FROM'],
+    'to': e['_STATE_TO'],
+    'created_at': e['_STATE_TS'],
+    'type': e['_STATE_TYPE'],
     'priority': 'normal',
-    'subject': '''$subject''',
-    'body': '''$body''',
+    'subject': e['_STATE_SUBJECT'],
+    'body': e['_STATE_BODY'],
     'source_ref': None,
     'expires_at': None
 }

ops/deploy.sh

@@ -43,7 +43,7 @@ echo "=== Pre-deploy syntax check ==="
 ERRORS=0
 for f in "$REPO_ROOT/ops/pipeline-v2/lib/"*.py "$REPO_ROOT/ops/pipeline-v2/"*.py "$REPO_ROOT/ops/diagnostics/"*.py; do
   [ -f "$f" ] || continue
-  if ! python3 -c "import ast; ast.parse(open('$f').read())" 2>/dev/null; then
+  if ! python3 -c "import ast, sys; ast.parse(open(sys.argv[1]).read())" "$f" 2>/dev/null; then
     echo "SYNTAX ERROR: $f"
     ERRORS=$((ERRORS + 1))
   fi

ops/research-session.sh

@@ -69,10 +69,9 @@ if [ ! -d "$REPO_DIR/.git" ]; then
 fi
 
 cd "$REPO_DIR"
-git config credential.helper "!f() { echo username=m3taversal; echo password=$FORGEJO_ADMIN_TOKEN; }; f"
 git remote set-url origin "${FORGEJO_URL}/teleo/teleo-codex.git" 2>/dev/null || true
-git checkout main >> "$LOG" 2>&1
-git pull --rebase >> "$LOG" 2>&1
+git -c http.extraHeader="Authorization: token $FORGEJO_ADMIN_TOKEN" checkout main >> "$LOG" 2>&1
+git -c http.extraHeader="Authorization: token $FORGEJO_ADMIN_TOKEN" pull --rebase >> "$LOG" 2>&1
 
 # --- Map agent to domain ---
 case "$AGENT" in
@@ -94,13 +93,13 @@ if [ ! -f "$NETWORK_FILE" ]; then
 else
     log "Pulling tweets from ${AGENT}'s network..."
     ACCOUNTS=$(python3 -c "
-import json
-with open('$NETWORK_FILE') as f:
+import json, sys
+with open(sys.argv[1]) as f:
     data = json.load(f)
 for acct in data.get('accounts', []):
     if acct.get('tier') in ('core', 'extended'):
         print(acct['username'])
-" 2>/dev/null || true)
+" "$NETWORK_FILE" 2>/dev/null || true)
 
     TWEET_DATA=""
     API_CALLS=0
@@ -132,7 +131,7 @@ for acct in data.get('accounts', []):
 $(python3 -c "
 import json, sys
 try:
-    d = json.load(open('$OUTFILE'))
+    d = json.load(open(sys.argv[1]))
     tweets = d.get('tweets', d.get('data', []))
     for t in tweets[:20]:
         text = t.get('text', '')[:500]
@@ -144,7 +143,7 @@ try:
         print()
 except Exception as e:
     print(f'Error reading: {e}', file=sys.stderr)
-" 2>/dev/null || echo "(failed to parse)")"
+" "$OUTFILE" 2>/dev/null || echo "(failed to parse)")"
         fi
     done
     log "API usage: ${API_CALLS} calls, ${API_CACHED} cached for ${AGENT}"
@@ -168,7 +167,7 @@ if [ -d "$INBOX_RAW" ] && ls "$INBOX_RAW"/*.json 2>/dev/null | head -1 > /dev/nu
 $(python3 -c "
 import json, sys
 try:
-    d = json.load(open('$RAWFILE'))
+    d = json.load(open(sys.argv[1]))
     tweets = d.get('tweets', d.get('data', []))
     for t in tweets[:20]:
         text = t.get('text', '')[:500]
@@ -180,7 +179,7 @@ try:
         print()
 except Exception as e:
     print(f'Error: {e}', file=sys.stderr)
-" 2>/dev/null || echo "(failed to parse)")"
+" "$RAWFILE" 2>/dev/null || echo "(failed to parse)")"
     done
 fi
 
@@ -432,7 +431,7 @@ git commit -m "${AGENT}: research session ${DATE} — ${SOURCE_COUNT} sources ar
 Pentagon-Agent: ${AGENT_UPPER} <HEADLESS>" >> "$LOG" 2>&1
 
 # --- Push ---
-git push -u origin "$BRANCH" --force >> "$LOG" 2>&1
+git -c http.extraHeader="Authorization: token $AGENT_TOKEN" push -u origin "$BRANCH" --force >> "$LOG" 2>&1
 log "Pushed $BRANCH"
 
 # --- Check for existing PR on this branch ---