fix: speed up handbook sync and stop llm_calls 404 noise

Handbook sync ran files sequentially under a 5 req/min limiter with a
hardcoded 60s LLM timeout, causing long syncs and AbortError timeouts on
large files. Now: limiter at 20 req/min, files processed with concurrency
4, handbook extraction timeout raised to 180s, and near-empty files skip
the LLM call.

callLLM gains a timeoutMs option; passing a signal no longer silently
disables the per-request timeout.

llm_calls telemetry self-disables after the first 404 so deploys without
the migration applied don't spam the console.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

src/components/admin/KnowledgeGraph.jsx

@@ -261,25 +261,53 @@ const KnowledgeGraph = () => {
         }
       });
 
-      setSyncResult({ added, modified, unchanged });
+      setSyncResult({ added, modified, unchanged, failed: [] });
 
       const filesToProcess = [...added, ...modified];
       if (filesToProcess.length > 0) {
-        setSyncProgress(`Processing 0 of ${filesToProcess.length} files...`);
-        let count = 0;
-        for (const file of filesToProcess) {
-          count++;
-          setSyncProgress(`Processing ${count} of ${filesToProcess.length}: ${file.name}...`);
+        const total = filesToProcess.length;
+        let done = 0;
+        const failed = [];
+        setSyncProgress(`Processing 0 of ${total} files...`);
+
+        // Run files in parallel with bounded concurrency. The extractionLimiter
+        // inside analyzeHandbookDelta still governs the actual API request rate;
+        // parallelism here just hides GitHub fetch latency and overlaps with the
+        // limiter's spacing instead of waiting serially.
+        const CONCURRENCY = 4;
+        const queue = filesToProcess.slice();
+
+        async function worker() {
+          while (queue.length > 0) {
+            const file = queue.shift();
+            if (!file) return;
             try {
               const rawContent = await getFileContent('respellion', 'employee-handbook', file.path);
-            // Pacing is handled centrally by extractionLimiter inside analyzeHandbookDelta.
+              // Skip near-empty files — they only burn an LLM call to extract nothing.
+              if (rawContent.trim().length < 50) {
+                await db.updateHandbookSyncState(file.path, file.sha);
+              } else {
                 await analyzeHandbookDelta(rawContent, file.path);
                 await db.updateHandbookSyncState(file.path, file.sha);
+              }
             } catch (err) {
               console.error('Failed to process file:', file.path, err);
+              failed.push({ path: file.path, message: err?.message || String(err) });
+            } finally {
+              done++;
+              setSyncProgress(`Processing ${done} of ${total} files (${failed.length} failed)...`);
             }
           }
-        setSyncProgress('Sync Complete! Click "Analyze & Optimize Graph" above to clean up and merge.');
+        }
+
+        await Promise.all(Array.from({ length: Math.min(CONCURRENCY, total) }, worker));
+
+        setSyncResult({ added, modified, unchanged, failed });
+        setSyncProgress(
+          failed.length === 0
+            ? 'Sync Complete! Click "Analyze & Optimize Graph" above to clean up and merge.'
+            : `Sync finished with ${failed.length} failure(s). See console for details.`
+        );
         reloadKb();
       }
 
@@ -461,6 +489,9 @@ ${JSON.stringify({ topics: compactTopics, relations: compactRelations })}`;
                 <p>Added files: {syncResult.added.length}</p>
                 <p>Modified files: {syncResult.modified.length}</p>
                 <p>Unchanged: {syncResult.unchanged.length}</p>
+                {syncResult.failed?.length > 0 && (
+                  <p className="text-red-600">Failed: {syncResult.failed.length}</p>
+                )}
               </div>
             )}
             {syncProgress && (

src/lib/extractionPipeline.js

@@ -67,6 +67,7 @@ export async function analyzeHandbookDelta(fileContent, filePath, { signal } = {
     tools: [EMIT_HANDBOOK_DELTA_TOOL],
     toolChoice: { type: 'tool', name: EMIT_HANDBOOK_DELTA_TOOL.name },
     maxTokens: 8192,
+    timeoutMs: 180_000,
     limiter: extractionLimiter,
     signal,
   });

src/lib/llm.js

@@ -112,9 +112,16 @@ function buildMessages({ messages, user }) {
   throw new Error('callLLM requires either `messages` or `user`.');
 }
 
+// Telemetry collection is optional. If the migration hasn't been applied on a
+// given deploy, the first POST returns 404; we then disable further attempts
+// to keep the console clean and avoid wasted round-trips.
+let llmCallsDisabled = false;
 function logLlmCall(record) {
+  if (llmCallsDisabled) return;
   try {
-    pb.collection('llm_calls').create(record).catch(() => {});
+    pb.collection('llm_calls').create(record).catch((err) => {
+      if (err?.status === 404) llmCallsDisabled = true;
+    });
   } catch {
     /* collection may not exist yet — swallow */
   }
@@ -271,6 +278,7 @@ function validateToolInputs(toolUses, task, toolSchemas) {
  * @property {Record<string, import('zod').ZodTypeAny>} [toolSchemas] Overrides for tool_use input validation.
  * @property {number} [maxTokens=4096]
  * @property {number} [temperature=0]
+ * @property {number} [timeoutMs=60000]  Per-request timeout in ms. Increase for large structured extractions.
  * @property {AbortSignal} [signal]
  * @property {{ acquire: (opts?:{signal?:AbortSignal}) => Promise<void>, pauseUntil: (untilMs:number) => void }} [limiter]
  */
@@ -291,6 +299,7 @@ export async function callLLM(options) {
     toolSchemas,
     maxTokens = 4096,
     temperature = 0,
+    timeoutMs = DEFAULT_TIMEOUT_MS,
     signal,
     limiter,
   } = options;
@@ -321,9 +330,9 @@ export async function callLLM(options) {
     result = await withRetry(
       async () => {
         if (limiter) await limiter.acquire({ signal });
-        const timeoutCtl = signal ? null : new AbortController();
-        const timer = timeoutCtl ? setTimeout(() => timeoutCtl.abort(new DOMException('Timeout', 'AbortError')), DEFAULT_TIMEOUT_MS) : null;
-        const fetchSignal = linkSignals(signal, timeoutCtl?.signal);
+        const timeoutCtl = new AbortController();
+        const timer = setTimeout(() => timeoutCtl.abort(new DOMException('Timeout', 'AbortError')), timeoutMs);
+        const fetchSignal = linkSignals(signal, timeoutCtl.signal);
 
         try {
           const response = await fetch(ANTHROPIC_URL, {

src/lib/llmRetry.js

@@ -160,10 +160,12 @@ export function createLimiter({ rps = 1, burst = 1 } = {}) {
 
 /**
  * Shared limiter for the multi-call extraction loops (source chunks,
- * handbook file sync). 5 requests/minute matches the lowest published
- * Anthropic tier so we stay well clear of 429.
+ * handbook file sync). 20 req/min sits comfortably under Anthropic Tier 1
+ * (50/min for Sonnet) and lets the handbook sync finish in a reasonable
+ * time without us redesigning the rate-limit story; if a 429 still slips
+ * through, `withRetry` honours Retry-After.
  */
-export const extractionLimiter = createLimiter({ rps: 5 / 60, burst: 1 });
+export const extractionLimiter = createLimiter({ rps: 20 / 60, burst: 2 });
 
 /**
  * Run `fn(attempt)` with retry. `fn` may throw a `RetryableError` to request