Code quality sweep: 30+ bug fixes, security hardening, and UX improvements (#507)

* Update waitlist, run ralph experiments

* fix PR files pagination: use octokit.paginate() for >100 files

* fix garbled FAQ answer on landing page

* track cache read/write tokens in OpenCode agent usage

* wrap dispatch() calls in try/catch to prevent webhook retries on transient failures

* replace raw error messages with generic responses in API routes

* guard request.json() calls with try-catch returning 400 on malformed bodies

* log warning when GraphQL review thread/comment counts hit pagination limits

* reduce review comment cache TTL from 24 hours to 10 minutes

* use select instead of include for proxyKey in workflow run queries

* align Claude agent activity timeout to 5 minutes to match OpenCode agent

* add in-memory dedup for PR close webhooks to prevent duplicate indexing

* extract isPullfrogLogin() helper for shared Pullfrog detection logic

* check response.ok on log fetch in checkSuite.ts

* add 10s timeouts to checkSuite API calls and log fetch

* parallelize proxy key usage API calls with Promise.allSettled

* fix three typos on landing page: colleage, dectects, reponse

* move MAX_STDERR_LINES constant to shared.ts

* add indexes on Repo.accountId and PFUser.accountId FK columns

* remove unused Permission enum from Prisma schema

* populate author and keywords in action/package.json

* use crypto.timingSafeEqual for all secret comparisons

* add missing env vars to globals.ts: R2, webhook, and API secrets

* remove commented-out UserRepo model from Prisma schema

* replace console.log/error with log utility in production API routes

* replace catch(error: any) with proper type guards in getUserRole

* remove stale TODO comment on console page

* handle repository_transferred webhook to update owner

* show toast.error instead of console.error on mode/workflow mutation failures

* add Space key handler for keyboard navigation on workflow run links

* replace role=link spans with button elements for proper accessibility

* add root 404 page with Pullfrog branding

* update ISSUES.md: mark completed items

* mark remaining low-priority UX items as addressed

* add error logging alongside toasts, add check script, update ralph commands

* address review feedback: squash migrations, fix try/catch scope, wire up globals consumers

- squash drop_permission_enum migration into add_indexes migration (one migration per PR)
- move getPullRequest() outside try/catch in mention handler so errors aren't mislogged as "dispatch failed"
- restore key ID in proxyKeys.ts Promise.allSettled error log
- remove accidental asdf.txt and ralph.md files
- wire up globals.ts exports to consumers (r2-uploads, r2-private, verifyHookdeckSignature, sync-usage, forwardPreviewWebhook, dispatch-workflow)

Made-with: Cursor

* update model snapshot (qwen3.6-plus-preview renamed to qwen3.6-plus)

Made-with: Cursor

mcp/checkSuite.ts

@@ -138,6 +138,7 @@ export function GetCheckSuiteLogsTool(ctx: ToolContext) {
           repo: ctx.repo.name,
           check_suite_id,
           per_page: 100,
+          request: { signal: AbortSignal.timeout(10_000) },
         }
       );
 
@@ -167,6 +168,7 @@ export function GetCheckSuiteLogsTool(ctx: ToolContext) {
           owner: ctx.repo.owner,
           repo: ctx.repo.name,
           run_id: run.id,
+          request: { signal: AbortSignal.timeout(10_000) },
         });
 
         // only process failed jobs
@@ -178,10 +180,17 @@ export function GetCheckSuiteLogsTool(ctx: ToolContext) {
               owner: ctx.repo.owner,
               repo: ctx.repo.name,
               job_id: job.id,
+              request: { signal: AbortSignal.timeout(10_000) },
             });
 
             const logsUrl = logsResponse.url;
-            const logsText = await fetch(logsUrl).then((r) => r.text());
+            const logsResult = await fetch(logsUrl, { signal: AbortSignal.timeout(10_000) });
+            if (!logsResult.ok) {
+              throw new Error(
+                `failed to fetch logs: ${logsResult.status} ${logsResult.statusText}`
+              );
+            }
+            const logsText = await logsResult.text();
 
             // write full log to disk
             const logPath = join(logsDir, `job-${job.id}.log`);

mcp/checkout.ts

@@ -157,13 +157,13 @@ type FetchPrDiffParams = {
  * this is the core diff formatting logic, extracted for testability.
  */
 export async function fetchAndFormatPrDiff(params: FetchPrDiffParams): Promise<FormatFilesResult> {
-  const filesResponse = await params.octokit.rest.pulls.listFiles({
+  const files = await params.octokit.paginate(params.octokit.rest.pulls.listFiles, {
     owner: params.owner,
     repo: params.repo,
     pull_number: params.pullNumber,
     per_page: 100,
   });
-  return formatFilesWithLineNumbers(filesResponse.data);
+  return formatFilesWithLineNumbers(files);
 }
 
 import type { GitContext } from "../utils/setup.ts";

mcp/reviewComments.ts

@@ -462,6 +462,19 @@ async function getReviewThreads(input: GetReviewDataInput) {
 
   const allThreads = response.repository?.pullRequest?.reviewThreads?.nodes ?? [];
 
+  if (allThreads.length >= 100) {
+    log.warning(
+      `PR ${input.owner}/${input.name}#${input.pullNumber}: reviewThreads returned 100 results (limit reached, some threads may be missing)`
+    );
+  }
+  for (const thread of allThreads) {
+    if (thread?.comments?.nodes && thread.comments.nodes.length >= 50) {
+      log.warning(
+        `PR ${input.owner}/${input.name}#${input.pullNumber}: review thread at ${thread.path}:${thread.line} has 50 comments (limit reached, some comments may be missing)`
+      );
+    }
+  }
+
   const threadsForReview = allThreads.filter((thread): thread is ReviewThread => {
     if (!thread?.comments?.nodes) return false;
     return thread.comments.nodes.some((c) => c?.pullRequestReview?.databaseId === input.reviewId);
@@ -511,13 +524,14 @@ export async function getReviewData(input: GetReviewDataInput): Promise<
   let threadBlocks: Array<{ path: string; lineRange: string; content: string[] }> = [];
 
   if (threads.length > 0) {
-    const prFilesResponse = await input.octokit.rest.pulls.listFiles({
+    const prFiles = await input.octokit.paginate(input.octokit.rest.pulls.listFiles, {
       owner: input.owner,
       repo: input.name,
       pull_number: input.pullNumber,
+      per_page: 100,
     });
     const filePatchMap = new Map<string, ParsedHunk[]>();
-    for (const file of prFilesResponse.data) {
+    for (const file of prFiles) {
       if (file.patch) {
         filePatchMap.set(file.filename, parseFilePatches(file.patch));
       }