diff --git a/scripts/epic-chain.sh b/scripts/epic-chain.sh
index 1a8cf1eaa..1087d2115 100755
--- a/scripts/epic-chain.sh
+++ b/scripts/epic-chain.sh
@@ -803,7 +803,7 @@ REPORT_GENERATED: $CHAIN_REPORT_FILE"
         log "Invoking report generator..."
 
         # Execute report generation
-        report_result=$(claude --dangerously-skip-permissions -p "$report_prompt" 2>&1) || true
+        report_result=$(env -u CLAUDECODE claude --dangerously-skip-permissions -p "$report_prompt" 2>&1) || true
 
         echo "$report_result" >> "$LOG_FILE"
 
diff --git a/scripts/epic-execute-lib/design-phase.sh b/scripts/epic-execute-lib/design-phase.sh
index 8a2b31cc2..33fab83fb 100644
--- a/scripts/epic-execute-lib/design-phase.sh
+++ b/scripts/epic-execute-lib/design-phase.sh
@@ -143,7 +143,7 @@ DESIGN COMPLETE: $story_id"
     fi
 
     local result
-    result=$(claude --dangerously-skip-permissions -p "$design_prompt" 2>&1) || true
+    result=$(env -u CLAUDECODE claude --dangerously-skip-permissions -p "$design_prompt" 2>&1) || true
 
     echo "$result" >> "$LOG_FILE"
 
diff --git a/scripts/epic-execute-lib/regression-gate.sh b/scripts/epic-execute-lib/regression-gate.sh
index 4bddb9661..af8b7ebe8 100644
--- a/scripts/epic-execute-lib/regression-gate.sh
+++ b/scripts/epic-execute-lib/regression-gate.sh
@@ -126,9 +126,9 @@ init_regression_baseline() {
 
             # Check if there's a test:json script for better parsing
             if grep -q '"test:json"' "$PROJECT_ROOT/package.json" 2>/dev/null; then
-                test_output=$(cd "$PROJECT_ROOT" && npm run test:json 2>&1) || true
+                test_output=$(cd "$PROJECT_ROOT" && run_with_timeout "${REGRESSION_TEST_TIMEOUT:-120}" npm run test:json) || true
             else
-                test_output=$(cd "$PROJECT_ROOT" && npm test 2>&1) || true
+                test_output=$(cd "$PROJECT_ROOT" && run_with_timeout "${REGRESSION_TEST_TIMEOUT:-120}" npm test) || true
             fi
 
             BASELINE_PASSING_TESTS=$(extract_test_count "$test_output")
@@ -152,14 +152,14 @@ init_regression_baseline() {
     elif [ -f "$PROJECT_ROOT/Cargo.toml" ]; then
         # Rust project
         log "Capturing baseline test count (Rust)..."
-        test_output=$(cd "$PROJECT_ROOT" && cargo test 2>&1) || true
+        test_output=$(cd "$PROJECT_ROOT" && run_with_timeout "${REGRESSION_TEST_TIMEOUT:-120}" cargo test) || true
         BASELINE_PASSING_TESTS=$(extract_test_count "$test_output")
         log "Baseline passing tests: $BASELINE_PASSING_TESTS"
 
     elif [ -f "$PROJECT_ROOT/go.mod" ]; then
         # Go project
         log "Capturing baseline test count (Go)..."
-        test_output=$(cd "$PROJECT_ROOT" && go test ./... -v 2>&1) || true
+        test_output=$(cd "$PROJECT_ROOT" && run_with_timeout "${REGRESSION_TEST_TIMEOUT:-120}" go test ./... -v) || true
         BASELINE_PASSING_TESTS=$(extract_test_count "$test_output")
         log "Baseline passing tests: $BASELINE_PASSING_TESTS"
 
@@ -167,7 +167,7 @@ init_regression_baseline() {
         # Python project
         if command -v pytest >/dev/null 2>&1; then
             log "Capturing baseline test count (Python)..."
-            test_output=$(cd "$PROJECT_ROOT" && pytest -v 2>&1) || true
+            test_output=$(cd "$PROJECT_ROOT" && run_with_timeout "${REGRESSION_TEST_TIMEOUT:-120}" pytest -v) || true
             BASELINE_PASSING_TESTS=$(extract_test_count "$test_output")
             log "Baseline passing tests: $BASELINE_PASSING_TESTS"
         fi
@@ -199,23 +199,23 @@ execute_regression_gate() {
     if [ -f "$PROJECT_ROOT/package.json" ]; then
         # Check if there's a test:json script for better parsing
         if grep -q '"test:json"' "$PROJECT_ROOT/package.json" 2>/dev/null; then
-            test_output=$(cd "$PROJECT_ROOT" && npm run test:json 2>&1) || true
+            test_output=$(cd "$PROJECT_ROOT" && run_with_timeout "${REGRESSION_TEST_TIMEOUT:-120}" npm run test:json) || true
         else
-            test_output=$(cd "$PROJECT_ROOT" && npm test 2>&1) || true
+            test_output=$(cd "$PROJECT_ROOT" && run_with_timeout "${REGRESSION_TEST_TIMEOUT:-120}" npm test) || true
         fi
         current_tests=$(extract_test_count "$test_output")
 
     elif [ -f "$PROJECT_ROOT/Cargo.toml" ]; then
-        test_output=$(cd "$PROJECT_ROOT" && cargo test 2>&1) || true
+        test_output=$(cd "$PROJECT_ROOT" && run_with_timeout "${REGRESSION_TEST_TIMEOUT:-120}" cargo test) || true
         current_tests=$(extract_test_count "$test_output")
 
     elif [ -f "$PROJECT_ROOT/go.mod" ]; then
-        test_output=$(cd "$PROJECT_ROOT" && go test ./... -v 2>&1) || true
+        test_output=$(cd "$PROJECT_ROOT" && run_with_timeout "${REGRESSION_TEST_TIMEOUT:-120}" go test ./... -v) || true
         current_tests=$(extract_test_count "$test_output")
 
     elif [ -f "$PROJECT_ROOT/requirements.txt" ] || [ -f "$PROJECT_ROOT/pyproject.toml" ]; then
         if command -v pytest >/dev/null 2>&1; then
-            test_output=$(cd "$PROJECT_ROOT" && pytest -v 2>&1) || true
+            test_output=$(cd "$PROJECT_ROOT" && run_with_timeout "${REGRESSION_TEST_TIMEOUT:-120}" pytest -v) || true
             current_tests=$(extract_test_count "$test_output")
         fi
     fi
diff --git a/scripts/epic-execute-lib/tdd-flow.sh b/scripts/epic-execute-lib/tdd-flow.sh
index bd041f728..903cffab2 100644
--- a/scripts/epic-execute-lib/tdd-flow.sh
+++ b/scripts/epic-execute-lib/tdd-flow.sh
@@ -169,7 +169,7 @@ After outputting the spec block:
     fi
 
     local result
-    result=$(claude --dangerously-skip-permissions -p "$spec_prompt" 2>&1) || true
+    result=$(env -u CLAUDECODE claude --dangerously-skip-permissions -p "$spec_prompt" 2>&1) || true
 
     echo "$result" >> "$LOG_FILE"
 
@@ -315,7 +315,7 @@ After implementing the tests:
     fi
 
     local result
-    result=$(claude --dangerously-skip-permissions -p "$impl_prompt" 2>&1) || true
+    result=$(env -u CLAUDECODE claude --dangerously-skip-permissions -p "$impl_prompt" 2>&1) || true
 
     echo "$result" >> "$LOG_FILE"
 
diff --git a/scripts/epic-execute-lib/utils.sh b/scripts/epic-execute-lib/utils.sh
index 6dadf3faa..61f8cd0fc 100644
--- a/scripts/epic-execute-lib/utils.sh
+++ b/scripts/epic-execute-lib/utils.sh
@@ -12,6 +12,41 @@
 # Usage: Sourced by epic-execute.sh
 #
 
+# =============================================================================
+# Portable Timeout Wrapper
+# =============================================================================
+
+# Run a command with a timeout (portable, no coreutils needed)
+# Usage: run_with_timeout <seconds> <command...>
+# Returns: command output via stdout; exit code 0 on success, 1 on timeout
+run_with_timeout() {
+    local timeout_secs="$1"; shift
+    local output_file
+    output_file=$(mktemp /tmp/bmad-timeout-XXXXXX)
+
+    ( "$@" > "$output_file" 2>&1 ) &
+    local cmd_pid=$!
+
+    ( sleep "$timeout_secs" && kill -TERM "$cmd_pid" 2>/dev/null && sleep 2 && kill -9 "$cmd_pid" 2>/dev/null ) &
+    local watchdog_pid=$!
+
+    wait "$cmd_pid" 2>/dev/null
+    local exit_code=$?
+
+    # Kill watchdog if command finished in time
+    kill "$watchdog_pid" 2>/dev/null
+    wait "$watchdog_pid" 2>/dev/null
+
+    cat "$output_file"
+    rm -f "$output_file"
+
+    # 143 = SIGTERM, 137 = SIGKILL (timed out)
+    if [ $exit_code -eq 143 ] || [ $exit_code -eq 137 ]; then
+        return 1
+    fi
+    return $exit_code
+}
+
 # =============================================================================
 # M1: Retry Logic with Exponential Backoff
 # =============================================================================
@@ -102,7 +137,7 @@ execute_claude_with_retry() {
 
     # Wrapper function for retry
     _claude_invoke() {
-        timeout "$timeout" claude --dangerously-skip-permissions -p "$1" 2>&1
+        timeout "$timeout" env -u CLAUDECODE claude --dangerously-skip-permissions -p "$1" 2>&1
         local code=$?
         if [ $code -eq 124 ]; then
             echo "TIMEOUT: Claude invocation timed out after ${timeout}s"
@@ -591,7 +626,7 @@ execute_claude_verbose() {
 
         # Execute with output tee'd to both terminal and log file
         local result
-        result=$(timeout "$timeout" claude --dangerously-skip-permissions -p "$prompt" 2>&1 | tee -a "$LOG_FILE")
+        result=$(timeout "$timeout" env -u CLAUDECODE claude --dangerously-skip-permissions -p "$prompt" 2>&1 | tee -a "$LOG_FILE")
         local exit_code=$?
 
         if [ $exit_code -eq 124 ]; then
@@ -605,7 +640,7 @@ execute_claude_verbose() {
     else
         # Non-verbose mode: capture output silently
         local result
-        result=$(timeout "$timeout" claude --dangerously-skip-permissions -p "$prompt" 2>&1)
+        result=$(timeout "$timeout" env -u CLAUDECODE claude --dangerously-skip-permissions -p "$prompt" 2>&1)
         local exit_code=$?
 
         # Log to file only
diff --git a/scripts/epic-execute.sh b/scripts/epic-execute.sh
index 42adea224..b7c0b8a86 100755
--- a/scripts/epic-execute.sh
+++ b/scripts/epic-execute.sh
@@ -249,6 +249,32 @@ save_log_to_repo() {
     fi
 }
 
+# Flush the current log to the repo after each story completes/fails.
+# Unlike save_log_to_repo (which runs once at exit), this overwrites
+# the same file incrementally so the repo always has the latest progress.
+flush_log_to_repo() {
+    # Skip if no log file or it's empty
+    if [ ! -f "$LOG_FILE" ] || [ ! -s "$LOG_FILE" ]; then
+        return 0
+    fi
+
+    # Create logs directory if needed
+    if [ -n "$LOGS_DIR" ]; then
+        mkdir -p "$LOGS_DIR" 2>/dev/null || true
+    else
+        return 0
+    fi
+
+    # Use a stable filename so each flush overwrites the previous snapshot
+    if [ -n "$EPIC_ID" ]; then
+        local flush_file="$LOGS_DIR/epic-${EPIC_ID}-latest.log"
+    else
+        return 0
+    fi
+
+    cp "$LOG_FILE" "$flush_file" 2>/dev/null || true
+}
+
 # =============================================================================
 # Git Safety Functions
 # =============================================================================
@@ -1394,7 +1420,7 @@ Do NOT use 'git add -A' or 'git add .' - only stage files you created or modifie
 
     # Execute in isolated context
     local result
-    result=$(claude --dangerously-skip-permissions -p "$dev_prompt" 2>&1) || true
+    result=$(env -u CLAUDECODE claude --dangerously-skip-permissions -p "$dev_prompt" 2>&1) || true
 
     echo "$result" >> "$LOG_FILE"
 
@@ -1534,7 +1560,7 @@ Stage any fixes with explicit file paths: git add <file1> <file2> ..."
 
     # Execute in isolated context
     local result
-    result=$(claude --dangerously-skip-permissions -p "$review_prompt" 2>&1) || true
+    result=$(env -u CLAUDECODE claude --dangerously-skip-permissions -p "$review_prompt" 2>&1) || true
 
     echo "$result" >> "$LOG_FILE"
 
@@ -1782,7 +1808,7 @@ Address all review findings now. This is attempt $attempt_num of 3."
             return 0
         fi
 
-        result=$(claude --dangerously-skip-permissions -f "$temp_prompt_file" 2>&1) || true
+        result=$(env -u CLAUDECODE claude --dangerously-skip-permissions -f "$temp_prompt_file" 2>&1) || true
         rm -f "$temp_prompt_file"
     else
         if [ "$DRY_RUN" = true ]; then
@@ -1791,7 +1817,7 @@ Address all review findings now. This is attempt $attempt_num of 3."
         fi
 
         # Execute in isolated context
-        result=$(claude --dangerously-skip-permissions -p "$fix_prompt" 2>&1) || true
+        result=$(env -u CLAUDECODE claude --dangerously-skip-permissions -p "$fix_prompt" 2>&1) || true
     fi
 
     echo "$result" >> "$LOG_FILE"
@@ -1930,7 +1956,7 @@ $build_output
         if grep -q '"test"' "$PROJECT_ROOT/package.json" 2>/dev/null; then
             log "Running tests..."
             local test_output
-            test_output=$(cd "$PROJECT_ROOT" && npm test 2>&1) || {
+            test_output=$(cd "$PROJECT_ROOT" && run_with_timeout "${REGRESSION_TEST_TIMEOUT:-120}" npm test) || {
                 local exit_code=$?
 
                 # Check if there are NEW failures (not just pre-existing baseline failures)
@@ -2248,7 +2274,7 @@ Stage any fixes with: git add <file1> <file2> ..."
     fi
 
     local result
-    result=$(claude --dangerously-skip-permissions -p "$arch_prompt" 2>&1) || true
+    result=$(env -u CLAUDECODE claude --dangerously-skip-permissions -p "$arch_prompt" 2>&1) || true
 
     echo "$result" >> "$LOG_FILE"
 
@@ -2325,7 +2351,7 @@ Stage any fixes with: git add <file1> <file2> ..."
     fi
 
     local result
-    result=$(claude --dangerously-skip-permissions -p "$quality_prompt" 2>&1) || true
+    result=$(env -u CLAUDECODE claude --dangerously-skip-permissions -p "$quality_prompt" 2>&1) || true
 
     echo "$result" >> "$LOG_FILE"
 
@@ -2460,7 +2486,7 @@ Analyze traceability now. Read story files on-demand as needed."
     fi
 
     local result
-    result=$(claude --dangerously-skip-permissions -p "$trace_prompt" 2>&1) || true
+    result=$(env -u CLAUDECODE claude --dangerously-skip-permissions -p "$trace_prompt" 2>&1) || true
 
     echo "$result" >> "$LOG_FILE"
 
@@ -2538,7 +2564,7 @@ Generate missing tests now."
     fi
 
     local result
-    result=$(claude --dangerously-skip-permissions -p "$fix_prompt" 2>&1) || true
+    result=$(env -u CLAUDECODE claude --dangerously-skip-permissions -p "$fix_prompt" 2>&1) || true
 
     echo "$result" >> "$LOG_FILE"
 
@@ -2892,7 +2918,7 @@ Generate the UAT document now. Read story files on-demand as needed."
     fi
 
     local result
-    result=$(claude --dangerously-skip-permissions -p "$uat_prompt" 2>&1) || true
+    result=$(env -u CLAUDECODE claude --dangerously-skip-permissions -p "$uat_prompt" 2>&1) || true
 
     echo "$result" >> "$LOG_FILE"
 
@@ -2988,6 +3014,8 @@ for story_file in "${STORIES[@]}"; do
             if type save_checkpoint >/dev/null 2>&1; then
                 save_checkpoint "$STORY_INDEX" "$story_id" "$COMPLETED" "$FAILED" "$SKIPPED"
             fi
+            # Flush log to repo after story failure
+            flush_log_to_repo
             continue
         fi
     else
@@ -3003,6 +3031,8 @@ for story_file in "${STORIES[@]}"; do
             if type save_checkpoint >/dev/null 2>&1; then
                 save_checkpoint "$STORY_INDEX" "$story_id" "$COMPLETED" "$FAILED" "$SKIPPED"
             fi
+            # Flush log to repo after story failure
+            flush_log_to_repo
             continue
         fi
     fi
@@ -3030,6 +3060,9 @@ for story_file in "${STORIES[@]}"; do
     if type save_checkpoint >/dev/null 2>&1; then
         save_checkpoint "$STORY_INDEX" "$story_id" "$COMPLETED" "$FAILED" "$SKIPPED"
     fi
+
+    # Flush log to repo after each completed story
+    flush_log_to_repo
 done
 
 # =============================================================================
diff --git a/scripts/uat-validate.sh b/scripts/uat-validate.sh
index 1181e1d6d..6f492e854 100755
--- a/scripts/uat-validate.sh
+++ b/scripts/uat-validate.sh
@@ -859,7 +859,7 @@ HUMAN_ACTION_NEEDED: {yes/no}"
 
     # Execute in isolated context
     local result
-    result=$(claude --dangerously-skip-permissions -p "$fix_prompt" 2>&1) || true
+    result=$(env -u CLAUDECODE claude --dangerously-skip-permissions -p "$fix_prompt" 2>&1) || true
 
     echo "$result" >> "$LOG_FILE"