fix: prefer active config when reading user settings (fixes #271)

Multiple "select from configs where userId" queries had no ORDER BY,
so when a user's database accidentally contained more than one config
row for the same user (e.g. from an env-loader insert path or a partial
default-config create), SQLite returned a non-deterministic row.

In the reported case this caused /api/config to hand back an empty stub
while /api/dashboard's repo/org counts came from the populated active
row. The dashboard's useConfigStatus hook then saw missing username/
token, treated config as incomplete, and never fetched dashboard data —
the UI rendered with all zeros even though 868 repos were sitting in
the database, mirroring fine in the background.

Add `ORDER BY isActive DESC, updatedAt DESC` before LIMIT 1 to every
"fetch the user's config" query so the active and most-recently-updated
row consistently wins. Also order env-config-loader's first-user pick
by createdAt for deterministic behavior across restarts.

Already-safe call sites that explicitly filter on isActive=true or
iterate all active configs (cleanup/scheduler/repositories/orgs/cleanup
trigger/sync-organization) are left unchanged.

Updates the mirror-repo test mock to match the new orderBy().limit()
chain.

Closes #271

src/lib/env-config-loader.ts

@@ -4,7 +4,7 @@
  */
 
 import { db, configs, users } from '@/lib/db';
-import { eq, and } from 'drizzle-orm';
+import { eq, and, sql } from 'drizzle-orm';
 import { v4 as uuidv4 } from 'uuid';
 import { encrypt } from '@/lib/utils/encryption';
 
@@ -224,10 +224,12 @@ export async function initializeConfigFromEnv(): Promise<void> {
 
     console.log('[ENV Config Loader] Found environment configuration, initializing...');
 
-    // Get the first user (admin user)
+    // Get the first user (admin user) — deterministic order so we always pick the
+    // same row across restarts even if multiple users exist.
     const firstUser = await db
       .select()
       .from(users)
+      .orderBy(sql`${users.createdAt} ASC`)
       .limit(1);
 
     if (firstUser.length === 0) {
@@ -237,11 +239,14 @@ export async function initializeConfigFromEnv(): Promise<void> {
 
     const userId = firstUser[0].id;
 
-    // Check if config already exists for this user
+    // Check if config already exists for this user — prefer the active config and
+    // fall back to most-recently-updated so we never write env values into a stale
+    // inactive stub while the populated active row sits untouched (see issue #271).
     const existingConfig = await db
       .select()
       .from(configs)
       .where(eq(configs.userId, userId))
+      .orderBy(sql`${configs.isActive} DESC`, sql`${configs.updatedAt} DESC`)
       .limit(1);
 
     // Determine mirror strategy based on environment variables or use explicit value

src/lib/notification-service.ts

@@ -3,7 +3,7 @@ import type { NotificationEvent } from "./providers/ntfy";
 import { sendNtfyNotification } from "./providers/ntfy";
 import { sendAppriseNotification } from "./providers/apprise";
 import { db, configs } from "@/lib/db";
-import { eq } from "drizzle-orm";
+import { eq, sql } from "drizzle-orm";
 import { decrypt } from "@/lib/utils/encryption";
 
 function sanitizeTestNotificationError(error: unknown): string {
@@ -120,11 +120,13 @@ export async function triggerJobNotification({
       return;
     }
 
-    // Fetch user's config from database
+    // Fetch user's config from database — prefer active and most-recently-updated
+    // to avoid picking a stale inactive stub when multiple rows exist (see issue #271).
     const configResults = await db
       .select()
       .from(configs)
       .where(eq(configs.userId, userId))
+      .orderBy(sql`${configs.isActive} DESC`, sql`${configs.updatedAt} DESC`)
       .limit(1);
 
     if (configResults.length === 0) {

src/lib/recovery.ts

@@ -5,7 +5,7 @@
 
 import { findInterruptedJobs, resumeInterruptedJob } from './helpers';
 import { db, repositories, organizations, mirrorJobs, configs } from './db';
-import { eq, and, lt, inArray } from 'drizzle-orm';
+import { eq, and, lt, inArray, sql } from 'drizzle-orm';
 import { mirrorGithubRepoToGitea, mirrorGitHubOrgRepoToGiteaOrg, syncGiteaRepo } from './gitea';
 import { createGitHubClient } from './github';
 import { processWithResilience } from './utils/concurrency';
@@ -216,11 +216,13 @@ async function recoverMirrorJob(job: any, remainingItemIds: string[]) {
   console.log(`Recovering mirror job ${job.id} with ${remainingItemIds.length} remaining items`);
 
   try {
-    // Get the config for this user with better error handling
+    // Get the config for this user — prefer active and most-recently-updated
+    // to avoid picking a stale inactive stub when multiple rows exist (see issue #271).
     const userConfigs = await db
       .select()
       .from(configs)
       .where(eq(configs.userId, job.userId))
+      .orderBy(sql`${configs.isActive} DESC`, sql`${configs.updatedAt} DESC`)
       .limit(1);
 
     if (userConfigs.length === 0) {
@@ -347,11 +349,13 @@ async function recoverSyncJob(job: any, remainingItemIds: string[]) {
   console.log(`Recovering sync job ${job.id} with ${remainingItemIds.length} remaining items`);
 
   try {
-    // Get the config for this user with better error handling
+    // Get the config for this user — prefer active and most-recently-updated
+    // to avoid picking a stale inactive stub when multiple rows exist (see issue #271).
     const userConfigs = await db
       .select()
       .from(configs)
       .where(eq(configs.userId, job.userId))
+      .orderBy(sql`${configs.isActive} DESC`, sql`${configs.updatedAt} DESC`)
       .limit(1);
 
     if (userConfigs.length === 0) {

src/lib/utils/config-defaults.ts

@@ -1,5 +1,5 @@
 import { db, configs } from "@/lib/db";
-import { eq } from "drizzle-orm";
+import { eq, sql } from "drizzle-orm";
 import { v4 as uuidv4 } from "uuid";
 import { encrypt } from "@/lib/utils/encryption";
 import { getNextScheduledRun, normalizeTimezone } from "@/lib/utils/schedule-utils";
@@ -25,11 +25,13 @@ export interface DefaultConfigOptions {
  * Environment variables can override these defaults
  */
 export async function createDefaultConfig({ userId, envOverrides = {} }: DefaultConfigOptions) {
-  // Check if config already exists
+  // Check if config already exists — prefer active and most-recently-updated
+  // to avoid returning a stale inactive stub when multiple rows exist (see issue #271).
   const existingConfig = await db
     .select()
     .from(configs)
     .where(eq(configs.userId, userId))
+    .orderBy(sql`${configs.isActive} DESC`, sql`${configs.updatedAt} DESC`)
     .limit(1);
 
   if (existingConfig.length > 0) {

src/pages/api/config/index.ts

@@ -1,7 +1,7 @@
 import type { APIRoute } from "astro";
 import { db, configs, users } from "@/lib/db";
 import { v4 as uuidv4 } from "uuid";
-import { eq } from "drizzle-orm";
+import { eq, sql } from "drizzle-orm";
 import { createSecureErrorResponse } from "@/lib/utils";
 import { 
   mapUiToDbConfig, 
@@ -83,11 +83,13 @@ export const POST: APIRoute = async ({ request, locals }) => {
       }
     }
 
-    // Fetch existing config
+    // Fetch existing config — prefer the active config; fall back to most-recently-updated
+    // so a stale inactive stub never wins over a populated active row (see issue #271).
     const existingConfigResult = await db
       .select()
       .from(configs)
       .where(eq(configs.userId, userId))
+      .orderBy(sql`${configs.isActive} DESC`, sql`${configs.updatedAt} DESC`)
       .limit(1);
 
     const existingConfig = existingConfigResult[0];
@@ -255,11 +257,14 @@ export const GET: APIRoute = async ({ request, locals }) => {
     if ("response" in authResult) return authResult.response;
     const userId = authResult.userId;
 
-    // Fetch the configuration for the user
+    // Fetch the configuration for the user — prefer the active config; fall back to
+    // most-recently-updated so a stale inactive stub never wins over a populated
+    // active row (see issue #271).
     const config = await db
       .select()
       .from(configs)
       .where(eq(configs.userId, userId))
+      .orderBy(sql`${configs.isActive} DESC`, sql`${configs.updatedAt} DESC`)
       .limit(1);
 
     if (config.length === 0) {

src/pages/api/dashboard/index.ts

@@ -38,7 +38,12 @@ export const GET: APIRoute = async ({ request, locals }) => {
         .where(eq(mirrorJobs.userId, userId))
         .orderBy(sql`${mirrorJobs.timestamp} DESC`)
         .limit(10),
-      db.select().from(configs).where(eq(configs.userId, userId)).limit(1),
+      db
+        .select()
+        .from(configs)
+        .where(eq(configs.userId, userId))
+        .orderBy(sql`${configs.isActive} DESC`, sql`${configs.updatedAt} DESC`)
+        .limit(1),
       db
         .select({ value: count() })
         .from(repositories)

src/pages/api/github/starred-lists.ts

@@ -1,6 +1,6 @@
 import type { APIRoute } from "astro";
 import { db, configs } from "@/lib/db";
-import { eq } from "drizzle-orm";
+import { eq, sql } from "drizzle-orm";
 import {
   createGitHubClient,
   getGithubStarredListNames,
@@ -15,10 +15,13 @@ export const GET: APIRoute = async ({ request, locals }) => {
     if ("response" in authResult) return authResult.response;
     const userId = authResult.userId;
 
+    // Prefer active and most-recently-updated config to avoid picking a stale
+    // inactive stub when multiple rows exist (see issue #271).
     const [config] = await db
       .select()
       .from(configs)
       .where(eq(configs.userId, userId))
+      .orderBy(sql`${configs.isActive} DESC`, sql`${configs.updatedAt} DESC`)
       .limit(1);
 
     if (!config) {

src/pages/api/job/approve-sync.ts

@@ -1,6 +1,6 @@
 import type { APIRoute } from "astro";
 import { db, configs, repositories } from "@/lib/db";
-import { and, eq, inArray } from "drizzle-orm";
+import { and, eq, inArray, sql } from "drizzle-orm";
 import { repositoryVisibilityEnum, repoStatusEnum } from "@/types/Repository";
 import { syncGiteaRepoEnhanced } from "@/lib/gitea-enhanced";
 import { createSecureErrorResponse } from "@/lib/utils";
@@ -38,11 +38,13 @@ export const POST: APIRoute = async ({ request, locals }) => {
       );
     }
 
-    // Fetch config
+    // Fetch config — prefer active and most-recently-updated to avoid picking
+    // a stale inactive stub when multiple rows exist (see issue #271).
     const configResult = await db
       .select()
       .from(configs)
       .where(eq(configs.userId, userId))
+      .orderBy(sql`${configs.isActive} DESC`, sql`${configs.updatedAt} DESC`)
       .limit(1);
 
     const config = configResult[0];

src/pages/api/job/mirror-org.ts

@@ -1,7 +1,7 @@
 import type { APIRoute } from "astro";
 import type { MirrorOrgRequest, MirrorOrgResponse } from "@/types/mirror";
 import { db, configs, organizations } from "@/lib/db";
-import { and, eq, inArray } from "drizzle-orm";
+import { and, eq, inArray, sql } from "drizzle-orm";
 import { createGitHubClient } from "@/lib/github";
 import { mirrorGitHubOrgToGitea } from "@/lib/gitea";
 import { repoStatusEnum } from "@/types/Repository";
@@ -41,11 +41,13 @@ export const POST: APIRoute = async ({ request, locals }) => {
       );
     }
 
-    // Fetch config
+    // Fetch config — prefer active and most-recently-updated to avoid picking
+    // a stale inactive stub when multiple rows exist (see issue #271).
     const configResult = await db
       .select()
       .from(configs)
       .where(eq(configs.userId, userId))
+      .orderBy(sql`${configs.isActive} DESC`, sql`${configs.updatedAt} DESC`)
       .limit(1);
 
     const config = configResult[0];

src/pages/api/job/mirror-repo.test.ts

@@ -3,6 +3,46 @@ import type { MirrorRepoRequest } from "@/types/mirror";
 import { POST } from "./mirror-repo";
 
 // Mock the database module
+const mockConfigRow = [{
+  id: "config-id",
+  userId: "user-id",
+  githubConfig: {
+    token: "github-token",
+    preserveOrgStructure: false,
+    mirrorIssues: false
+  },
+  giteaConfig: {
+    url: "https://gitea.example.com",
+    token: "gitea-token",
+    username: "giteauser"
+  }
+}];
+
+const mockRepoRows = [
+  {
+    id: "repo-id-1",
+    name: "test-repo-1",
+    visibility: "public",
+    status: "pending",
+    organization: null,
+    lastMirrored: null,
+    errorMessage: null,
+    forkedFrom: null,
+    mirroredLocation: ""
+  },
+  {
+    id: "repo-id-2",
+    name: "test-repo-2",
+    visibility: "public",
+    status: "pending",
+    organization: null,
+    lastMirrored: null,
+    errorMessage: null,
+    forkedFrom: null,
+    mirroredLocation: ""
+  }
+];
+
 const mockDb = {
   select: mock(() => ({
     from: mock((table: any) => ({
@@ -10,47 +50,14 @@ const mockDb = {
         // Return config for configs table
         if (table === mockConfigs) {
           return {
-            limit: mock(() => Promise.resolve([{
-              id: "config-id",
-              userId: "user-id",
-              githubConfig: {
-                token: "github-token",
-                preserveOrgStructure: false,
-                mirrorIssues: false
-              },
-              giteaConfig: {
-                url: "https://gitea.example.com",
-                token: "gitea-token",
-                username: "giteauser"
-              }
-            }]))
+            orderBy: mock(() => ({
+              limit: mock(() => Promise.resolve(mockConfigRow))
+            })),
+            limit: mock(() => Promise.resolve(mockConfigRow))
           };
         }
         // Return repositories for repositories table
-        return Promise.resolve([
-          {
-            id: "repo-id-1",
-            name: "test-repo-1",
-            visibility: "public",
-            status: "pending",
-            organization: null,
-            lastMirrored: null,
-            errorMessage: null,
-            forkedFrom: null,
-            mirroredLocation: ""
-          },
-          {
-            id: "repo-id-2",
-            name: "test-repo-2",
-            visibility: "public",
-            status: "pending",
-            organization: null,
-            lastMirrored: null,
-            errorMessage: null,
-            forkedFrom: null,
-            mirroredLocation: ""
-          }
-        ]);
+        return Promise.resolve(mockRepoRows);
       })
     }))
   }))

src/pages/api/job/mirror-repo.ts

@@ -1,7 +1,7 @@
 import type { APIRoute } from "astro";
 import type { MirrorRepoRequest, MirrorRepoResponse } from "@/types/mirror";
 import { db, configs, repositories } from "@/lib/db";
-import { and, eq, inArray } from "drizzle-orm";
+import { and, eq, inArray, sql } from "drizzle-orm";
 import { repositoryVisibilityEnum, repoStatusEnum } from "@/types/Repository";
 import {
   mirrorGithubRepoToGitea,
@@ -43,11 +43,13 @@ export const POST: APIRoute = async ({ request, locals }) => {
       );
     }
 
-    // Fetch config
+    // Fetch config — prefer active and most-recently-updated to avoid picking
+    // a stale inactive stub when multiple rows exist (see issue #271).
     const configResult = await db
       .select()
       .from(configs)
       .where(eq(configs.userId, userId))
+      .orderBy(sql`${configs.isActive} DESC`, sql`${configs.updatedAt} DESC`)
       .limit(1);
 
     const config = configResult[0];

src/pages/api/job/reset-metadata.ts

@@ -1,5 +1,5 @@
 import type { APIRoute } from "astro";
-import { and, eq, inArray } from "drizzle-orm";
+import { and, eq, inArray, sql } from "drizzle-orm";
 import { db, configs, repositories } from "@/lib/db";
 import { repositoryVisibilityEnum, repoStatusEnum } from "@/types/Repository";
 import type { ResetMetadataRequest, ResetMetadataResponse } from "@/types/reset-metadata";
@@ -35,10 +35,13 @@ export const POST: APIRoute = async ({ request, locals }) => {
       );
     }
 
+    // Prefer active and most-recently-updated config to avoid picking a stale
+    // inactive stub when multiple rows exist (see issue #271).
     const configResult = await db
       .select()
       .from(configs)
       .where(eq(configs.userId, userId))
+      .orderBy(sql`${configs.isActive} DESC`, sql`${configs.updatedAt} DESC`)
       .limit(1);
 
     const config = configResult[0];

src/pages/api/job/retry-repo.ts

@@ -1,6 +1,6 @@
 import type { APIRoute } from "astro";
 import { db, configs, repositories } from "@/lib/db";
-import { and, eq, inArray } from "drizzle-orm";
+import { and, eq, inArray, sql } from "drizzle-orm";
 import { getGiteaRepoOwnerAsync, isRepoPresentInGitea } from "@/lib/gitea";
 import {
   mirrorGithubRepoToGitea,
@@ -45,11 +45,13 @@ export const POST: APIRoute = async ({ request, locals }) => {
       );
     }
 
-    // Fetch user config
+    // Fetch user config — prefer active and most-recently-updated to avoid picking
+    // a stale inactive stub when multiple rows exist (see issue #271).
     const configResult = await db
       .select()
       .from(configs)
       .where(eq(configs.userId, userId))
+      .orderBy(sql`${configs.isActive} DESC`, sql`${configs.updatedAt} DESC`)
       .limit(1);
 
     const config = configResult[0];

src/pages/api/job/schedule-sync-repo.ts

@@ -1,6 +1,6 @@
 import type { APIRoute } from "astro";
 import { db, configs, repositories } from "@/lib/db";
-import { and, eq, or } from "drizzle-orm";
+import { and, eq, or, sql } from "drizzle-orm";
 import { repoStatusEnum, repositoryVisibilityEnum } from "@/types/Repository";
 import { isRepoPresentInGitea, syncGiteaRepo } from "@/lib/gitea";
 import type {
@@ -19,11 +19,13 @@ export const POST: APIRoute = async ({ request, locals }) => {
 
     await request.json().catch(() => ({} as ScheduleSyncRepoRequest));
 
-    // Fetch config for the user
+    // Fetch config for the user — prefer active and most-recently-updated to avoid
+    // picking a stale inactive stub when multiple rows exist (see issue #271).
     const configResult = await db
       .select()
       .from(configs)
       .where(eq(configs.userId, userId))
+      .orderBy(sql`${configs.isActive} DESC`, sql`${configs.updatedAt} DESC`)
       .limit(1);
 
     const config = configResult[0];

src/pages/api/job/sync-repo.ts

@@ -1,7 +1,7 @@
 import type { APIRoute } from "astro";
 import type { MirrorRepoRequest } from "@/types/mirror";
 import { db, configs, repositories } from "@/lib/db";
-import { and, eq, inArray } from "drizzle-orm";
+import { and, eq, inArray, sql } from "drizzle-orm";
 import { repositoryVisibilityEnum, repoStatusEnum } from "@/types/Repository";
 import { syncGiteaRepo } from "@/lib/gitea";
 import type { SyncRepoResponse } from "@/types/sync";
@@ -38,11 +38,13 @@ export const POST: APIRoute = async ({ request, locals }) => {
       );
     }
 
-    // Fetch config
+    // Fetch config — prefer active and most-recently-updated to avoid picking
+    // a stale inactive stub when multiple rows exist (see issue #271).
     const configResult = await db
       .select()
       .from(configs)
       .where(eq(configs.userId, userId))
+      .orderBy(sql`${configs.isActive} DESC`, sql`${configs.updatedAt} DESC`)
       .limit(1);
 
     const config = configResult[0];

src/pages/api/rate-limit/index.ts

@@ -1,6 +1,6 @@
 import type { APIRoute } from "astro";
 import { db, rateLimits } from "@/lib/db";
-import { eq, and, desc } from "drizzle-orm";
+import { eq, and, desc, sql } from "drizzle-orm";
 import { jsonResponse, createSecureErrorResponse } from "@/lib/utils";
 import { RateLimitManager } from "@/lib/rate-limit-manager";
 import { createGitHubClient } from "@/lib/github";
@@ -19,10 +19,13 @@ export const GET: APIRoute = async ({ request, locals }) => {
   try {
     // If refresh is requested, fetch current rate limit from GitHub
     if (refresh) {
+      // Prefer active and most-recently-updated config to avoid picking a stale
+      // inactive stub when multiple rows exist (see issue #271).
       const [config] = await db
         .select()
         .from(configs)
         .where(eq(configs.userId, userId))
+        .orderBy(sql`${configs.isActive} DESC`, sql`${configs.updatedAt} DESC`)
         .limit(1);
 
       if (config && config.githubConfig?.token) {

src/pages/api/sync/index.ts

@@ -1,6 +1,6 @@
 import type { APIRoute } from "astro";
 import { db, organizations, repositories, configs } from "@/lib/db";
-import { eq, and } from "drizzle-orm";
+import { eq, and, sql } from "drizzle-orm";
 import { v4 as uuidv4 } from "uuid";
 import { createMirrorJob } from "@/lib/helpers";
 import {
@@ -21,10 +21,13 @@ export const POST: APIRoute = async ({ request, locals }) => {
   const userId = authResult.userId;
 
   try {
+    // Prefer active and most-recently-updated config to avoid picking a stale
+    // inactive stub when multiple rows exist (see issue #271).
     const [config] = await db
       .select()
       .from(configs)
       .where(eq(configs.userId, userId))
+      .orderBy(sql`${configs.isActive} DESC`, sql`${configs.updatedAt} DESC`)
       .limit(1);
 
     if (!config) {

src/pages/api/sync/repository.ts

@@ -2,7 +2,7 @@ import type { APIRoute } from "astro";
 import { Octokit } from "@octokit/rest";
 import { configs, db, repositories } from "@/lib/db";
 import { v4 as uuidv4 } from "uuid";
-import { and, eq } from "drizzle-orm";
+import { and, eq, sql } from "drizzle-orm";
 import { type Repository } from "@/lib/db/schema";
 import { jsonResponse, createSecureErrorResponse } from "@/lib/utils";
 import type {
@@ -72,11 +72,13 @@ export const POST: APIRoute = async ({ request, locals }) => {
       });
     }
 
-    // Get user's active config
+    // Get user's active config — prefer active and most-recently-updated to avoid
+    // picking a stale inactive stub when multiple rows exist (see issue #271).
     const [config] = await db
       .select()
       .from(configs)
       .where(eq(configs.userId, userId))
+      .orderBy(sql`${configs.isActive} DESC`, sql`${configs.updatedAt} DESC`)
       .limit(1);
 
     if (!config) {