diff --git a/.agents/scripts/headless-runtime-helper.sh b/.agents/scripts/headless-runtime-helper.sh
index d4649bab7d..fad8b1b4c8 100755
--- a/.agents/scripts/headless-runtime-helper.sh
+++ b/.agents/scripts/headless-runtime-helper.sh
@@ -222,6 +222,13 @@ get_session_id() {
 	return 0
 }
 
+clear_session_id() {
+	local provider="$1"
+	local session_key="$2"
+	db_query "DELETE FROM provider_sessions WHERE provider = '$(sql_escape "$provider")' AND session_key = '$(sql_escape "$session_key")';" >/dev/null
+	return 0
+}
+
 store_session_id() {
 	local provider="$1"
 	local session_key="$2"
@@ -671,10 +678,18 @@ cmd_run() {
 		return 1
 	}
 
-	local selected_model provider persisted_session
+	local selected_model provider persisted_session=""
 	selected_model=$(choose_model "$role" "$model_override") || return $?
 	provider=$(extract_provider "$selected_model")
-	persisted_session=$(get_session_id "$provider" "$session_key")
+	if [[ "$role" == "pulse" ]]; then
+		# Pulse runs must start from the current pre-fetched state each cycle.
+		# Reusing a prior OpenCode session contaminates later /pulse runs with
+		# stale conversational context, which leads to idle watchdog kills and an
+		# empty worker pool. Workers still keep session reuse.
+		clear_session_id "$provider" "$session_key"
+	else
+		persisted_session=$(get_session_id "$provider" "$session_key")
+	fi
 
 	local -a cmd=("$OPENCODE_BIN_DEFAULT" run "$prompt" --dir "$work_dir" -m "$selected_model" --title "$title" --format json)
 	if [[ -n "$agent_name" ]]; then
@@ -704,7 +719,7 @@ cmd_run() {
 			print_warning "$provider returned exit 0 without any model activity; backing off provider"
 			return 75
 		fi
-		if [[ -n "$discovered_session" ]]; then
+		if [[ "$role" != "pulse" && -n "$discovered_session" ]]; then
 			store_session_id "$provider" "$session_key" "$discovered_session" "$selected_model"
 		fi
 		rm -f "$output_file"
diff --git a/setup.sh b/setup.sh
index 8cfc27bd22..722a8e8805 100755
--- a/setup.sh
+++ b/setup.sh
@@ -112,6 +112,21 @@ _cron_escape() {
 	return 0
 }
 
+# Resolve the canonical main worktree path for the current repo.
+# When setup.sh is run from a linked worktree, launchd/cron should still point
+# autonomous services at the main repo checkout, not the feature worktree.
+_resolve_main_worktree_dir() {
+	local repo_dir="$1"
+	local main_worktree=""
+	main_worktree=$(git -C "$repo_dir" worktree list --porcelain 2>/dev/null | awk '/^worktree / {print substr($0, 10); exit}') || main_worktree=""
+	if [[ -n "$main_worktree" && -d "$main_worktree" ]]; then
+		printf '%s' "$main_worktree"
+		return 0
+	fi
+	printf '%s' "$repo_dir"
+	return 0
+}
+
 # Ensure the crontab has a single PATH= line at the top with the current $PATH.
 # Individual cron entries must NOT set inline PATH= — it overrides the global one
 # and hardcodes system-specific paths (nvm, bun, cargo, etc.). This function
@@ -840,8 +855,9 @@ main() {
 	#   - Non-interactive: only installs if config explicitly says true
 	local wrapper_script="$HOME/.aidevops/agents/scripts/pulse-wrapper.sh"
 	local pulse_label="com.aidevops.aidevops-supervisor-pulse"
-	local _aidevops_dir
+	local _aidevops_dir _pulse_repo_dir
 	_aidevops_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+	_pulse_repo_dir=$(_resolve_main_worktree_dir "$_aidevops_dir")
 
 	# Read explicit user consent from config.jsonc (not merged defaults).
 	# Empty = user never configured this; "true"/"false" = explicit choice.
@@ -959,7 +975,7 @@ main() {
 			_xml_wrapper_script=$(_xml_escape "$wrapper_script")
 			_xml_home=$(_xml_escape "$HOME")
 			_xml_opencode_bin=$(_xml_escape "$opencode_bin")
-			_xml_aidevops_dir=$(_xml_escape "$_aidevops_dir")
+			_xml_aidevops_dir=$(_xml_escape "$_pulse_repo_dir")
 			_xml_path=$(_xml_escape "$PATH")
 			if [[ -n "${AIDEVOPS_HEADLESS_MODELS:-}" ]]; then
 				local _xml_headless_models
@@ -1035,7 +1051,7 @@ PLIST
 			# via $(…) or backticks if paths contain shell metacharacters
 			local _cron_opencode_bin _cron_aidevops_dir _cron_wrapper_script _cron_headless_env=""
 			_cron_opencode_bin=$(_cron_escape "$opencode_bin")
-			_cron_aidevops_dir=$(_cron_escape "$_aidevops_dir")
+			_cron_aidevops_dir=$(_cron_escape "$_pulse_repo_dir")
 			_cron_wrapper_script=$(_cron_escape "$wrapper_script")
 			if [[ -n "${AIDEVOPS_HEADLESS_MODELS:-}" ]]; then
 				local _cron_headless_models
diff --git a/tests/test-headless-runtime-helper.sh b/tests/test-headless-runtime-helper.sh
index a911ed0e6b..aab2375e29 100755
--- a/tests/test-headless-runtime-helper.sh
+++ b/tests/test-headless-runtime-helper.sh
@@ -148,6 +148,29 @@ else
 	fail "second run reuses persisted provider session" "logged args: $(tr '\n' ' ' <"$STUB_LOG_FILE")"
 fi
 
+section "Pulse Runs Stay Fresh"
+export STUB_SESSION_ID="ses_pulse_one"
+rm -f "$STUB_LOG_FILE"
+AIDEVOPS_HEADLESS_PROVIDER_ALLOWLIST=openai bash "$HELPER" run \
+	--role pulse \
+	--session-key supervisor-pulse \
+	--dir "$REPO_DIR" \
+	--title "Supervisor Pulse" \
+	--prompt "/pulse" >/dev/null
+export STUB_SESSION_ID="ses_pulse_two"
+AIDEVOPS_HEADLESS_PROVIDER_ALLOWLIST=openai bash "$HELPER" run \
+	--role pulse \
+	--session-key supervisor-pulse \
+	--dir "$REPO_DIR" \
+	--title "Supervisor Pulse" \
+	--prompt "/pulse" >/dev/null
+
+if grep -q -- '--session ' "$STUB_LOG_FILE"; then
+	fail "pulse runs do not reuse persisted sessions" "logged args: $(tr '\n' ' ' <"$STUB_LOG_FILE")"
+else
+	pass "pulse runs do not reuse persisted sessions"
+fi
+
 section "Zero Activity Success Is Rejected"
 export STUB_EMIT_ACTIVITY="0"
 if AIDEVOPS_HEADLESS_PROVIDER_ALLOWLIST=openai bash "$HELPER" run \