dapdevsoftware · deividi86 · Feb 23, 2026
diff --git a/CLAUDE.md b/CLAUDE.md
@@ -15,6 +15,8 @@ The system consists of main bash scripts and a modular library system designed f
 ### Main Scripts
 
 1. **smithers_loop.sh** - The main autonomous research loop that executes Claude Code repeatedly
+   - Checks graceful exit conditions BEFORE circuit breaker to ensure completion is detected first
+   - Exit priority: evidence-based completion → permission denials → minimum loops → exit_signal → safety limits
 2. **smithers_monitor.sh** - Live monitoring dashboard for tracking research progress
 3. **setup.sh** - Project initialization script for new Smithers research projects
 4. **smithers_import.sh** - Research brief import tool that converts documents to Smithers format
@@ -59,6 +61,8 @@ The system uses a modular architecture with research-focused components:
 
 5. **lib/circuit_breaker.sh** - Research-Specific Stagnation Detection
    - Three states: CLOSED (normal), HALF_OPEN (monitoring), OPEN (halted)
+   - Recognizes SYNTHESIS.md creation/updates as evidence of research progress
+   - Won't open when research is complete (calls `is_research_complete()` as safety net)
    - Research thresholds:
      - `CB_SEARCH_REPETITION_THRESHOLD=3` - Repeated identical searches
      - `CB_NO_NEW_SOURCES_THRESHOLD=5` - Loops without new sources
@@ -69,6 +73,7 @@ The system uses a modular architecture with research-focused components:
 6. **lib/response_analyzer.sh** - Intelligent Research Response Analysis
    - Analyzes Claude Code output for completion signals
    - Detects SMITHERS_STATUS blocks with research-specific fields
+   - `exit_signal` from `.response_analysis` is read directly by `should_exit_gracefully()`
    - Research patterns: `PHASE_COMPLETE_PATTERNS`, `RESEARCH_COMPLETE_PATTERNS`
    - Session management with `.smithers/.smithers_session`
 
@@ -123,6 +128,22 @@ Smithers enforces a 5-phase research methodology:
 - Provide actionable recommendations
 - Requirements: All prior phases complete
 
+### Research Completion Detection
+Research is considered complete when any of these conditions are met (checked in order):
+1. **SYNTHESIS.md marker**: File containing `RESEARCH_COMPLETE` (case-insensitive) found in any of: `.smithers/evidence/SYNTHESIS.md`, `.smithers/SYNTHESIS.md`, or `SYNTHESIS.md` at project root
+2. **Phase status**: `current_phase == "COMPLETE"` in `phases/status.json`
+3. **Threshold-based**: In SYNTHESIZE phase with all evidence thresholds met (12+ sources, 15+ claims, 6+ validations)
+
+### Exit Priority Order
+The loop checks completion conditions in this priority:
+1. **Evidence-Based Completion** (PRIORITY 0): `is_research_complete()` — bypasses minimum loops
+2. **Permission Denials** (PRIORITY 1): Blocked tools requiring `.smithersrc` updates
+3. **Minimum Loops** (PRIORITY 2): Must reach `MIN_RESEARCH_LOOPS` (default: 3)
+4. **Exit Signal** (PRIORITY 3): Claude set `EXIT_SIGNAL: true` in SMITHERS_STATUS
+5. **Safety Limits** (PRIORITY 4): Test-only loop stagnation detection
+
+Graceful exit is checked BEFORE the circuit breaker to prevent false stagnation halts.
+
 ## Key Commands
 
 ### Installation

diff --git a/lib/circuit_breaker.sh b/lib/circuit_breaker.sh
@@ -201,6 +201,21 @@ record_loop_result() {
             [[ "${VERBOSE_PROGRESS:-}" == "true" ]] && echo "DEBUG: Research progress - phase: $last_phase -> $current_phase" >&2
         fi
     fi
+
+    # Check if SYNTHESIS.md was created or updated (research completion artifact)
+    if [[ -f "$SMITHERS_DIR/evidence/SYNTHESIS.md" ]]; then
+        local synthesis_mtime
+        synthesis_mtime=$(stat -c %Y "$SMITHERS_DIR/evidence/SYNTHESIS.md" 2>/dev/null || \
+                          stat -f %m "$SMITHERS_DIR/evidence/SYNTHESIS.md" 2>/dev/null || echo 0)
+        local last_synthesis_mtime=$(cat "$SMITHERS_DIR/.last_synthesis_mtime" 2>/dev/null || echo 0)
+        synthesis_mtime=$((synthesis_mtime + 0))
+        last_synthesis_mtime=$((last_synthesis_mtime + 0))
+        if [[ $synthesis_mtime -gt $last_synthesis_mtime ]]; then
+            research_progress=true
+            echo "$synthesis_mtime" > "$SMITHERS_DIR/.last_synthesis_mtime"
+            [[ "${VERBOSE_PROGRESS:-}" == "true" ]] && echo "DEBUG: Research progress - SYNTHESIS.md updated" >&2
+        fi
+    fi
     # =========================================================================
 
     # Determine if progress was made
@@ -229,6 +244,18 @@ record_loop_result() {
         consecutive_no_progress=$((consecutive_no_progress + 1))
     fi
 
+    # SAFETY: If research is complete, force progress=true to prevent CB from opening
+    # This handles the case where research is done but no new files are being created
+    if [[ "$has_progress" != "true" ]] && type is_research_complete &>/dev/null 2>&1; then
+        local _phases_file="$SMITHERS_DIR/phases/status.json"
+        local _evidence_dir="$SMITHERS_DIR/evidence"
+        if [[ -f "$_phases_file" ]] && [[ $(is_research_complete "$_phases_file" "$_evidence_dir") == "true" ]]; then
+            has_progress=true
+            consecutive_no_progress=0
+            [[ "${VERBOSE_PROGRESS:-}" == "true" ]] && echo "DEBUG: Research complete - overriding no-progress" >&2
+        fi
+    fi
+
     # Detect same error repetition
     if [[ "$has_errors" == "true" ]]; then
         consecutive_same_error=$((consecutive_same_error + 1))

diff --git a/lib/phase_state_machine.sh b/lib/phase_state_machine.sh
@@ -240,13 +240,21 @@ is_research_complete() {
 
     # PRIMARY CHECK: SYNTHESIS.md with RESEARCH_COMPLETE marker = done
     # This is the ground truth - if Claude wrote this, research is complete
-    local synthesis_file="$evidence_dir/SYNTHESIS.md"
-    if [[ -f "$synthesis_file" ]]; then
-        if grep -q "RESEARCH_COMPLETE" "$synthesis_file" 2>/dev/null; then
-            echo "true"
-            return 0
+    # Check multiple locations where Claude might write the synthesis
+    local synthesis_locations=(
+        "$evidence_dir/SYNTHESIS.md"
+        "${evidence_dir%/*}/SYNTHESIS.md"
+        "SYNTHESIS.md"
+    )
+
+    for synthesis_file in "${synthesis_locations[@]}"; do
+        if [[ -f "$synthesis_file" ]]; then
+            if grep -qi "RESEARCH_COMPLETE" "$synthesis_file" 2>/dev/null; then
+                echo "true"
+                return 0
+            fi
         fi
-    fi
+    done
 
     # FALLBACK: Phase-based completion (legacy)
     if [[ "$current_phase" == "COMPLETE" ]]; then

diff --git a/smithers_loop.sh b/smithers_loop.sh
@@ -303,7 +303,7 @@ setup_tmux_session() {
     # Split right pane horizontally (top: Claude output, bottom: status)
     tmux split-window -v -t "$session_name:0.1" -c "$project_dir"
 
-    # Right-top pane (pane 1): Live Claude Code output
+    # Right-top pane (pane 1): Live research output
     tmux send-keys -t "$session_name:0.1" "tail -f '$project_dir/$LIVE_LOG_FILE'" Enter
 
     # Right-bottom pane (pane 2): Smithers status monitor
@@ -322,8 +322,9 @@ setup_tmux_session() {
         smithers_cmd="'$smithers_home/smithers_loop.sh'"
     fi
 
-    # Always use --live mode in tmux for real-time streaming
-    smithers_cmd="$smithers_cmd --live"
+    # Note: --live streaming mode (stdbuf | tee | jq pipeline) is fragile and can
+    # cause Claude to receive SIGSTOP. Background mode works reliably with the
+    # tail -f pane already providing real-time output via the log file.
 
     # Forward --calls if non-default
     if [[ "$MAX_CALLS_PER_HOUR" != "100" ]]; then
@@ -570,7 +571,23 @@ should_exit_gracefully() {
     fi
 
     # =================================================================
-    # PRIORITY 2: Safety limits (prevent infinite loops)
+    # PRIORITY 3: Direct exit_signal from response analysis
+    # If Claude explicitly signaled EXIT_SIGNAL: true in its output,
+    # respect it as a completion signal.
+    # =================================================================
+    if [[ -f "$RESPONSE_ANALYSIS_FILE" ]]; then
+        local exit_signal=$(jq -r '.analysis.exit_signal // false' "$RESPONSE_ANALYSIS_FILE" 2>/dev/null || echo "false")
+        if [[ "$exit_signal" == "true" ]]; then
+            local evidence_counts=$(get_evidence_counts)
+            log_status "SUCCESS" "Exit condition: Claude exit signal (exit_signal=true)" >&2
+            log_status "INFO" "Evidence: $evidence_counts" >&2
+            echo "exit_signal"
+            return 0
+        fi
+    fi
+
+    # =================================================================
+    # PRIORITY 4: Safety limits (prevent infinite loops)
     # =================================================================
     if [[ ! -f "$EXIT_SIGNALS_FILE" ]]; then
         echo ""
@@ -779,15 +796,15 @@ init_claude_session() {
         # Handle stat failure (-1) - treat as needing new session
         # Don't expire sessions when we can't determine age
         if [[ $age_hours -eq -1 ]]; then
-            log_status "WARN" "Could not determine session age, starting new session"
+            log_status "WARN" "Could not determine session age, starting new session" >&2
             rm -f "$CLAUDE_SESSION_FILE"
             echo ""
             return 0
         fi
 
         # Check if session has expired
         if [[ $age_hours -ge $CLAUDE_SESSION_EXPIRY_HOURS ]]; then
-            log_status "INFO" "Session expired (${age_hours}h old, max ${CLAUDE_SESSION_EXPIRY_HOURS}h), starting new session"
+            log_status "INFO" "Session expired (${age_hours}h old, max ${CLAUDE_SESSION_EXPIRY_HOURS}h), starting new session" >&2
             rm -f "$CLAUDE_SESSION_FILE"
             echo ""
             return 0
@@ -796,13 +813,13 @@ init_claude_session() {
         # Session is valid, try to read it
         local session_id=$(cat "$CLAUDE_SESSION_FILE" 2>/dev/null)
         if [[ -n "$session_id" ]]; then
-            log_status "INFO" "Resuming Claude session: ${session_id:0:20}... (${age_hours}h old)"
+            log_status "INFO" "Resuming Claude session: ${session_id:0:20}... (${age_hours}h old)" >&2
             echo "$session_id"
             return 0
         fi
     fi
 
-    log_status "INFO" "Starting new Claude session"
+    log_status "INFO" "Starting new Claude session" >&2
     echo ""
 }
 
@@ -1049,6 +1066,15 @@ build_claude_command() {
         CLAUDE_CMD_ARGS+=("--output-format" "json")
     fi
 
+    # Auto-approve tool use for allowed tools (prevents interactive permission prompts)
+    local perm_mode="${CLAUDE_PERMISSION_MODE:-acceptEdits}"
+    case "$perm_mode" in
+        acceptEdits|default|plan) ;;
+        *) log_status "WARN" "Invalid CLAUDE_PERMISSION_MODE '$perm_mode', using 'acceptEdits'" >&2
+           perm_mode="acceptEdits" ;;
+    esac
+    CLAUDE_CMD_ARGS+=("--permission-mode" "$perm_mode")
+
     # Add allowed tools (each tool as separate array element)
     if [[ -n "$CLAUDE_ALLOWED_TOOLS" ]]; then
         CLAUDE_CMD_ARGS+=("--allowedTools")
@@ -1066,7 +1092,11 @@ build_claude_command() {
 
     # Add session continuity flag
     if [[ "$CLAUDE_USE_CONTINUE" == "true" ]]; then
-        CLAUDE_CMD_ARGS+=("--continue")
+        if [[ -n "$session_id" ]]; then
+            CLAUDE_CMD_ARGS+=("--resume" "$session_id")
+        else
+            CLAUDE_CMD_ARGS+=("--continue")
+        fi
     fi
 
     # Add loop context as system prompt (no escaping needed - array handles it)
@@ -1376,6 +1406,9 @@ execute_claude_code() {
                 last_line=$(tail -1 "$output_file" 2>/dev/null | head -c 80)
                 # Copy to live.log for tmux monitoring
                 cp "$output_file" "$LIVE_LOG_FILE" 2>/dev/null
+            else
+                # Output file empty (JSON mode buffers until done) — show waiting status
+                echo -e "$(date '+%H:%M:%S') $progress_indicator Phase: $(get_current_phase) | Claude working... (${progress_counter}0s)" >> "$LIVE_LOG_FILE"
             fi
 
             # Update progress file for monitor
@@ -1415,6 +1448,23 @@ EOF
 
         log_status "SUCCESS" "✅ Claude Code execution completed successfully"
 
+        # Write research summary to live.log for tmux monitoring
+        {
+            echo ""
+            echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━"
+            echo "  Loop #$loop_count completed — $(date '+%Y-%m-%d %H:%M:%S')"
+            echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━"
+            # Extract the result text from JSON output
+            local result_text
+            result_text=$(jq -r '.result // empty' "$output_file" 2>/dev/null)
+            if [[ -n "$result_text" ]]; then
+                echo "$result_text"
+            else
+                echo "(No result text in output)"
+            fi
+            echo ""
+        } > "$LIVE_LOG_FILE"
+
         # Save session ID from JSON output
         if [[ "$CLAUDE_USE_CONTINUE" == "true" ]]; then
             save_claude_session "$output_file"
@@ -1572,16 +1622,8 @@ main() {
             break
         fi
 
-        # Check circuit breaker before attempting execution
-        if should_halt_execution; then
-            reset_session "circuit_breaker_open"
-            update_status "$loop_count" "$(cat "$CALL_COUNT_FILE")" "circuit_breaker_open" "halted" "stagnation_detected"
-            log_status "ERROR" "🛑 Circuit breaker has opened - execution halted"
-            break
-        fi
-
-        # Check for graceful exit conditions BEFORE rate limiting
-        # This ensures we exit even if rate limited with research complete
+        # Check for graceful exit conditions BEFORE circuit breaker
+        # This ensures research completion is detected before the CB can halt the loop
         local exit_reason=$(should_exit_gracefully)
         if [[ "$exit_reason" != "" ]]; then
             # Handle permission_denied specially
@@ -1642,6 +1684,14 @@ main() {
             break
         fi
 
+        # Check circuit breaker after graceful exit conditions
+        if should_halt_execution; then
+            reset_session "circuit_breaker_open"
+            update_status "$loop_count" "$(cat "$CALL_COUNT_FILE")" "circuit_breaker_open" "halted" "stagnation_detected"
+            log_status "ERROR" "🛑 Circuit breaker has opened - execution halted"
+            break
+        fi
+
         # Check rate limits (AFTER exit conditions so we can exit even when rate limited)
         if ! can_make_call; then
             wait_for_reset

diff --git a/smithers_status.sh b/smithers_status.sh
@@ -69,7 +69,7 @@ if [[ -f "$SYNTHESIS_FILE" ]]; then
     echo "   Modified: $MODIFIED"
 
     # Check for completion markers
-    if grep -q "RESEARCH_COMPLETE" "$SYNTHESIS_FILE" 2>/dev/null; then
+    if grep -qi "RESEARCH_COMPLETE" "$SYNTHESIS_FILE" 2>/dev/null; then
         echo -e "${GREEN}✅ Contains RESEARCH_COMPLETE marker${NC}"
         COMPLETE=true
     else