fix: requestId dedup to prevent ~2x cost overcounting + stale session detection

Manually ported from upstream:
- ef2e0868: deduplicate streaming JSONL entries by requestId
- 4f21f267: mark stale ongoing sessions as dead after 5min inactivity

src/main/services/discovery/ProjectScanner.ts

@@ -984,6 +984,12 @@ export class ProjectScanner {
         ? firstMessageTimestampMs
         : birthtimeMs;
 
+    // If messages suggest ongoing but the file hasn't been written to in 5+ minutes,
+    // the session likely crashed/was killed (upstream fix #94)
+    const STALE_SESSION_THRESHOLD_MS = 5 * 60 * 1000;
+    const isOngoing =
+      metadata.isOngoing && Date.now() - effectiveMtime < STALE_SESSION_THRESHOLD_MS;
+
     return {
       id: sessionId,
       projectId,
@@ -993,7 +999,7 @@ export class ProjectScanner {
       messageTimestamp: metadata.firstUserMessage?.timestamp,
       hasSubagents,
       messageCount: metadata.messageCount,
-      isOngoing: metadata.isOngoing,
+      isOngoing,
       gitBranch: metadata.gitBranch ?? undefined,
       metadataLevel,
       contextConsumption: metadata.contextConsumption,

src/main/types/messages.ts

@@ -103,6 +103,8 @@ export interface ParsedMessage {
   toolUseResult?: ToolUseResultData;
   /** Whether this is a compact summary boundary message */
   isCompactSummary?: boolean;
+  /** API request ID for deduplicating streaming entries */
+  requestId?: string;
 }
 
 // =============================================================================

src/main/utils/jsonl.ts

@@ -125,6 +125,7 @@ function parseChatHistoryEntry(entry: ChatHistoryEntry): ParsedMessage | null {
   let role: string | undefined;
   let usage: TokenUsage | undefined;
   let model: string | undefined;
+  let requestId: string | undefined;
   let cwd: string | undefined;
   let gitBranch: string | undefined;
   let agentId: string | undefined;
@@ -163,6 +164,7 @@ function parseChatHistoryEntry(entry: ChatHistoryEntry): ParsedMessage | null {
       usage = entry.message.usage;
       model = entry.message.model;
       agentId = entry.agentId;
+      requestId = entry.requestId;
     } else if (entry.type === 'system') {
       isMeta = entry.isMeta ?? false;
     }
@@ -195,6 +197,7 @@ function parseChatHistoryEntry(entry: ChatHistoryEntry): ParsedMessage | null {
     sourceToolUseID,
     sourceToolAssistantUUID,
     toolUseResult,
+    requestId,
   };
 }
 
@@ -221,24 +224,61 @@ function parseMessageType(type?: string): MessageType | null {
   }
 }
 
+// =============================================================================
+// Streaming Deduplication
+// =============================================================================
+
+/**
+ * Deduplicate streaming assistant entries by requestId.
+ *
+ * Claude Code writes multiple JSONL entries per API response during streaming,
+ * each with the same requestId but incrementally increasing output_tokens.
+ * Only the last entry per requestId has the final, complete token counts.
+ *
+ * Messages without a requestId (user, system, etc.) pass through unchanged.
+ * Returns a new array with only the last entry per requestId kept.
+ */
+export function deduplicateByRequestId(messages: ParsedMessage[]): ParsedMessage[] {
+  const lastIndexByRequestId = new Map<string, number>();
+  for (let i = 0; i < messages.length; i++) {
+    const rid = messages[i].requestId;
+    if (rid) {
+      lastIndexByRequestId.set(rid, i);
+    }
+  }
+
+  if (lastIndexByRequestId.size === 0) {
+    return messages;
+  }
+
+  return messages.filter((msg, i) => {
+    if (!msg.requestId) return true;
+    return lastIndexByRequestId.get(msg.requestId) === i;
+  });
+}
+
 // =============================================================================
 // Metrics Calculation
 // =============================================================================
 
 /**
  * Calculate session metrics from parsed messages.
+ * Deduplicates streaming entries by requestId before summing to avoid ~2x cost overcounting.
  */
 export function calculateMetrics(messages: ParsedMessage[]): SessionMetrics {
   if (messages.length === 0) {
     return { ...EMPTY_METRICS };
   }
 
+  // Deduplicate streaming entries: keep only the last entry per requestId
+  const dedupedMessages = deduplicateByRequestId(messages);
+
   let inputTokens = 0;
   let outputTokens = 0;
   let cacheReadTokens = 0;
   let cacheCreationTokens = 0;
 
-  // Get timestamps for duration (loop instead of Math.min/max spread to avoid stack overflow on large sessions)
+  // Get timestamps for duration from ALL messages (not deduped) for accurate session length
   const timestamps = messages.map((m) => m.timestamp.getTime()).filter((t) => !isNaN(t));
 
   let minTime = 0;
@@ -255,7 +295,7 @@ export function calculateMetrics(messages: ParsedMessage[]): SessionMetrics {
   // Calculate cost per-message, then sum (tiered pricing applies per-API-call, not to aggregated totals)
   let costUsd = 0;
 
-  for (const msg of messages) {
+  for (const msg of dedupedMessages) {
     if (msg.usage) {
       const msgInputTokens = msg.usage.input_tokens ?? 0;
       const msgOutputTokens = msg.usage.output_tokens ?? 0;