diff --git a/apps/server/src/becca/becca-interface.ts b/apps/server/src/becca/becca-interface.ts
index 7620ef3f5..005a5cc52 100644
--- a/apps/server/src/becca/becca-interface.ts
+++ b/apps/server/src/becca/becca-interface.ts
@@ -251,7 +251,7 @@ export default class Becca {
     getAllNoteSet() {
         // caching this since it takes 10s of milliseconds to fill this initial NoteSet for many notes
         if (!this.allNoteSetCache) {
-            const allNotes = [];
+            const allNotes: BNote[] = [];
 
             for (const noteId in this.notes) {
                 const note = this.notes[noteId];
diff --git a/apps/server/src/becca/becca_service.ts b/apps/server/src/becca/becca_service.ts
index 8f54728ca..92967da34 100644
--- a/apps/server/src/becca/becca_service.ts
+++ b/apps/server/src/becca/becca_service.ts
@@ -76,7 +76,7 @@ function getNoteTitleArrayForPath(notePathArray: string[]) {
         return [getNoteTitle(notePathArray[0])];
     }
 
-    const titles = [];
+    const titles: string[] = [];
 
     let parentNoteId = "root";
     let hoistedNotePassed = false;
diff --git a/apps/server/src/becca/entities/bnote.ts b/apps/server/src/becca/entities/bnote.ts
index 3813b5bbc..570d1b7b7 100644
--- a/apps/server/src/becca/entities/bnote.ts
+++ b/apps/server/src/becca/entities/bnote.ts
@@ -388,7 +388,7 @@ class BNote extends AbstractBeccaEntity<BNote> {
                 }
             }
 
-            const templateAttributes = [];
+            const templateAttributes: BAttribute[] = [];
 
             for (const ownedAttr of parentAttributes) {
                 // parentAttributes so we process also inherited templates
diff --git a/apps/server/src/becca/similarity.ts b/apps/server/src/becca/similarity.ts
index 8f4bdf0ff..fe7ecda21 100644
--- a/apps/server/src/becca/similarity.ts
+++ b/apps/server/src/becca/similarity.ts
@@ -254,7 +254,7 @@ function hasConnectingRelation(sourceNote: BNote, targetNote: BNote) {
 }
 
 async function findSimilarNotes(noteId: string): Promise<SimilarNote[] | undefined> {
-    const results = [];
+    const results: SimilarNote[] = [];
     let i = 0;
 
     const baseNote = becca.notes[noteId];
diff --git a/apps/server/src/routes/api/note_map.ts b/apps/server/src/routes/api/note_map.ts
index f621c7b2f..470152bd6 100644
--- a/apps/server/src/routes/api/note_map.ts
+++ b/apps/server/src/routes/api/note_map.ts
@@ -12,6 +12,11 @@ interface Backlink {
     excerpts?: string[];
 }
 
+interface TreeLink {
+    sourceNoteId: string;
+    targetNoteId: string;
+}
+
 function buildDescendantCountMap(noteIdsToCount: string[]) {
     if (!Array.isArray(noteIdsToCount)) {
         throw new Error("noteIdsToCount: type error");
@@ -50,7 +55,7 @@ function getNeighbors(note: BNote, depth: number): string[] {
         return [];
     }
 
-    const retNoteIds = [];
+    const retNoteIds: string[] = [];
 
     function isIgnoredRelation(relation: BAttribute) {
         return ["relationMapLink", "template", "inherit", "image", "ancestor"].includes(relation.name);
@@ -196,7 +201,7 @@ function getTreeMap(req: Request) {
     const noteIds = new Set<string>();
     notes.forEach(([noteId]) => noteId && noteIds.add(noteId));
 
-    const links = [];
+    const links: TreeLink[] = [];
 
     for (const { parentNoteId, childNoteId } of subtree.relationships) {
         if (!noteIds.has(parentNoteId) || !noteIds.has(childNoteId)) {
@@ -246,7 +251,7 @@ function findExcerpts(sourceNote: BNote, referencedNoteId: string) {
     const html = sourceNote.getContent();
     const document = new JSDOM(html).window.document;
 
-    const excerpts = [];
+    const excerpts: string[] = [];
 
     removeImages(document);
 
diff --git a/apps/server/src/routes/api/options.ts b/apps/server/src/routes/api/options.ts
index 3a0a9b06b..c69f7568f 100644
--- a/apps/server/src/routes/api/options.ts
+++ b/apps/server/src/routes/api/options.ts
@@ -9,6 +9,12 @@ import { changeLanguage, getLocales } from "../../services/i18n.js";
 import type { OptionNames } from "@triliumnext/commons";
 import config from "../../services/config.js";
 
+interface UserTheme {
+    val: string; // value of the theme, used in the URL
+    title: string; // title of the theme, displayed in the UI
+    noteId: string; // ID of the note containing the theme
+}
+
 // options allowed to be updated directly in the Options dialog
 const ALLOWED_OPTIONS = new Set<OptionNames>([
     "eraseEntitiesAfterTimeInSeconds",
@@ -177,7 +183,7 @@ function update(name: string, value: string) {
 
 function getUserThemes() {
     const notes = searchService.searchNotes("#appTheme", { ignoreHoistedNote: true });
-    const ret = [];
+    const ret: UserTheme[] = [];
 
     for (const note of notes) {
         let value = note.getOwnedLabelValue("appTheme");
diff --git a/apps/server/src/routes/api/recent_changes.ts b/apps/server/src/routes/api/recent_changes.ts
index 67b7436a0..1e539710e 100644
--- a/apps/server/src/routes/api/recent_changes.ts
+++ b/apps/server/src/routes/api/recent_changes.ts
@@ -21,7 +21,7 @@ interface RecentChangeRow {
 function getRecentChanges(req: Request) {
     const { ancestorNoteId } = req.params;
 
-    let recentChanges = [];
+    let recentChanges: RecentChangeRow[] = [];
 
     const revisionRows = sql.getRows<RecentChangeRow>(`
         SELECT
diff --git a/apps/server/src/routes/api/script.ts b/apps/server/src/routes/api/script.ts
index c702a82d8..d9d2fac8f 100644
--- a/apps/server/src/routes/api/script.ts
+++ b/apps/server/src/routes/api/script.ts
@@ -1,6 +1,6 @@
 "use strict";
 
-import scriptService from "../../services/script.js";
+import scriptService, { type Bundle } from "../../services/script.js";
 import attributeService from "../../services/attributes.js";
 import becca from "../../becca/becca.js";
 import syncService from "../../services/sync.js";
@@ -54,7 +54,7 @@ function run(req: Request) {
 function getBundlesWithLabel(label: string, value?: string) {
     const notes = attributeService.getNotesWithLabel(label, value);
 
-    const bundles = [];
+    const bundles: Bundle[] = [];
 
     for (const note of notes) {
         const bundle = scriptService.getScriptBundleForFrontend(note);
@@ -97,7 +97,7 @@ function getRelationBundles(req: Request) {
     const targetNoteIds = filtered.map((relation) => relation.value);
     const uniqueNoteIds = Array.from(new Set(targetNoteIds));
 
-    const bundles = [];
+    const bundles: Bundle[] = [];
 
     for (const noteId of uniqueNoteIds) {
         const note = becca.getNoteOrThrow(noteId);
diff --git a/apps/server/src/routes/api/sql.ts b/apps/server/src/routes/api/sql.ts
index ce2fc5127..0a1fbb28d 100644
--- a/apps/server/src/routes/api/sql.ts
+++ b/apps/server/src/routes/api/sql.ts
@@ -6,9 +6,14 @@ import type { Request } from "express";
 import ValidationError from "../../errors/validation_error.js";
 import { safeExtractMessageAndStackFromError } from "../../services/utils.js";
 
+interface Table {
+    name: string;
+    columns: unknown[];
+}
+
 function getSchema() {
-    const tableNames = sql.getColumn(/*sql*/`SELECT name FROM sqlite_master WHERE type='table' AND name NOT LIKE 'sqlite_%' ORDER BY name`);
-    const tables = [];
+    const tableNames = sql.getColumn<string>(/*sql*/`SELECT name FROM sqlite_master WHERE type='table' AND name NOT LIKE 'sqlite_%' ORDER BY name`);
+    const tables: Table[] = [];
 
     for (const tableName of tableNames) {
         tables.push({
@@ -31,7 +36,7 @@ function execute(req: Request) {
     const queries = content.split("\n---");
 
     try {
-        const results = [];
+        const results: unknown[] = [];
 
         for (let query of queries) {
             query = query.trim();
diff --git a/apps/server/src/routes/api/tree.ts b/apps/server/src/routes/api/tree.ts
index 885529c93..bd6c9bb61 100644
--- a/apps/server/src/routes/api/tree.ts
+++ b/apps/server/src/routes/api/tree.ts
@@ -5,6 +5,7 @@ import log from "../../services/log.js";
 import NotFoundError from "../../errors/not_found_error.js";
 import type { Request } from "express";
 import type BNote from "../../becca/entities/bnote.js";
+import type { AttributeRow, BranchRow, NoteRow } from "@triliumnext/commons";
 
 function getNotesAndBranchesAndAttributes(_noteIds: string[] | Set<string>) {
     const noteIds = new Set(_noteIds);
@@ -53,7 +54,7 @@ function getNotesAndBranchesAndAttributes(_noteIds: string[] | Set<string>) {
         collectEntityIds(note);
     }
 
-    const notes = [];
+    const notes: NoteRow[] = [];
 
     for (const noteId of collectedNoteIds) {
         const note = becca.notes[noteId];
@@ -68,7 +69,7 @@ function getNotesAndBranchesAndAttributes(_noteIds: string[] | Set<string>) {
         });
     }
 
-    const branches = [];
+    const branches: BranchRow[] = [];
 
     if (noteIds.has("root")) {
         branches.push({
@@ -99,7 +100,7 @@ function getNotesAndBranchesAndAttributes(_noteIds: string[] | Set<string>) {
         });
     }
 
-    const attributes = [];
+    const attributes: AttributeRow[] = [];
 
     for (const attributeId of collectedAttributeIds) {
         const attribute = becca.attributes[attributeId];
diff --git a/apps/server/src/services/content_hash.ts b/apps/server/src/services/content_hash.ts
index 0247bd335..6c8365e2b 100644
--- a/apps/server/src/services/content_hash.ts
+++ b/apps/server/src/services/content_hash.ts
@@ -7,6 +7,11 @@ import eraseService from "./erase.js";
 
 type SectorHash = Record<string, string>;
 
+interface FailedCheck {
+    entityName: string;
+    sector: string[1];
+}
+
 function getEntityHashes() {
     // blob erasure is not synced, we should check before each sync if there's some blob to erase
     eraseService.eraseUnusedBlobs();
@@ -56,7 +61,7 @@ function getEntityHashes() {
 
 function checkContentHashes(otherHashes: Record<string, SectorHash>) {
     const entityHashes = getEntityHashes();
-    const failedChecks = [];
+    const failedChecks: FailedCheck[] = [];
 
     for (const entityName in entityHashes) {
         const thisSectorHashes: SectorHash = entityHashes[entityName] || {};
diff --git a/apps/server/src/services/llm/context/code_handlers.ts b/apps/server/src/services/llm/context/code_handlers.ts
index f4b1fca97..6a7d0f7af 100644
--- a/apps/server/src/services/llm/context/code_handlers.ts
+++ b/apps/server/src/services/llm/context/code_handlers.ts
@@ -160,7 +160,7 @@ function extractJsStructure(content: string): string {
     }
 
     // Look for class declarations
-    const classes = [];
+    const classes: string[] = [];
     for (let i = 0; i < lines.length; i++) {
         const line = lines[i].trim();
         if (line.startsWith('class ') || line.includes(' class ')) {
@@ -173,7 +173,7 @@ function extractJsStructure(content: string): string {
     }
 
     // Look for function declarations
-    const functions = [];
+    const functions: string[] = [];
     for (let i = 0; i < lines.length; i++) {
         const line = lines[i].trim();
         if (line.startsWith('function ') ||
@@ -212,7 +212,7 @@ function extractPythonStructure(content: string): string {
     }
 
     // Look for class declarations
-    const classes = [];
+    const classes: string[] = [];
     for (let i = 0; i < lines.length; i++) {
         const line = lines[i].trim();
         if (line.startsWith('class ')) {
@@ -225,7 +225,7 @@ function extractPythonStructure(content: string): string {
     }
 
     // Look for function declarations
-    const functions = [];
+    const functions: string[] = [];
     for (let i = 0; i < lines.length; i++) {
         const line = lines[i].trim();
         if (line.startsWith('def ')) {
@@ -263,7 +263,7 @@ function extractClassBasedStructure(content: string): string {
     }
 
     // Look for class declarations
-    const classes = [];
+    const classes: string[] = [];
     for (let i = 0; i < lines.length; i++) {
         const line = lines[i].trim();
         if (line.match(/^(public|private|protected)?\s*(class|interface|enum)\s+\w+/)) {
@@ -276,7 +276,7 @@ function extractClassBasedStructure(content: string): string {
     }
 
     // Look for method declarations
-    const methods = [];
+    const methods: string[] = [];
     for (let i = 0; i < lines.length; i++) {
         const line = lines[i].trim();
         if (line.match(/^(public|private|protected)?\s*(static)?\s*[\w<>[\]]+\s+\w+\s*\(/)) {
@@ -319,7 +319,7 @@ function extractGoStructure(content: string): string {
     }
 
     // Look for type declarations (structs, interfaces)
-    const types = [];
+    const types: string[] = [];
     for (let i = 0; i < lines.length; i++) {
         const line = lines[i].trim();
         if (line.startsWith('type ') && (line.includes(' struct ') || line.includes(' interface '))) {
@@ -332,7 +332,7 @@ function extractGoStructure(content: string): string {
     }
 
     // Look for function declarations
-    const functions = [];
+    const functions: string[] = [];
     for (let i = 0; i < lines.length; i++) {
         const line = lines[i].trim();
         if (line.startsWith('func ')) {
@@ -366,7 +366,7 @@ function extractRustStructure(content: string): string {
     }
 
     // Look for struct/enum/trait declarations
-    const types = [];
+    const types: string[] = [];
     for (let i = 0; i < lines.length; i++) {
         const line = lines[i].trim();
         if (line.startsWith('struct ') || line.startsWith('enum ') || line.startsWith('trait ')) {
@@ -379,8 +379,8 @@ function extractRustStructure(content: string): string {
     }
 
     // Look for function/impl declarations
-    const functions = [];
-    const impls = [];
+    const functions: string[] = [];
+    const impls: string[] = [];
 
     for (let i = 0; i < lines.length; i++) {
         const line = lines[i].trim();
diff --git a/apps/server/src/services/llm/context/content_chunking.ts b/apps/server/src/services/llm/context/content_chunking.ts
index a9f032684..0e57da515 100644
--- a/apps/server/src/services/llm/context/content_chunking.ts
+++ b/apps/server/src/services/llm/context/content_chunking.ts
@@ -198,7 +198,7 @@ export async function semanticChunking(
 
     // Try to split on headers first
     const headerPattern = /#{1,6}\s+.+|<h[1-6][^>]*>.*?<\/h[1-6]>/g;
-    const sections = [];
+    const sections: string[] = [];
 
     let lastIndex = 0;
     let match;
diff --git a/apps/server/src/services/llm/context_extractors/query_decomposition_tool.ts b/apps/server/src/services/llm/context_extractors/query_decomposition_tool.ts
index 2e65ada76..917403abb 100644
--- a/apps/server/src/services/llm/context_extractors/query_decomposition_tool.ts
+++ b/apps/server/src/services/llm/context_extractors/query_decomposition_tool.ts
@@ -439,7 +439,7 @@ export class QueryDecompositionTool {
 
         // If no pattern match, try to extract noun phrases
         const words = query.split(/\s+/);
-        const potentialEntities = [];
+        const potentialEntities: string[] = [];
         let currentPhrase = '';
 
         for (const word of words) {
diff --git a/apps/server/src/services/llm/embeddings/base_embeddings.ts b/apps/server/src/services/llm/embeddings/base_embeddings.ts
index ffc57174c..0332bbf51 100644
--- a/apps/server/src/services/llm/embeddings/base_embeddings.ts
+++ b/apps/server/src/services/llm/embeddings/base_embeddings.ts
@@ -246,7 +246,7 @@ export abstract class BaseEmbeddingProvider {
      */
     protected generateNoteContextText(context: NoteEmbeddingContext): string {
         // Build a relationship-focused summary first
-        const relationshipSummary = [];
+        const relationshipSummary: string[] = [];
 
         // Summarize the note's place in the hierarchy
         if (context.parentTitles.length > 0) {
diff --git a/apps/server/src/services/llm/embeddings/queue.ts b/apps/server/src/services/llm/embeddings/queue.ts
index 1b27559d1..6b3b5e415 100644
--- a/apps/server/src/services/llm/embeddings/queue.ts
+++ b/apps/server/src/services/llm/embeddings/queue.ts
@@ -13,6 +13,21 @@ import indexService from '../index_service.js';
 // Track which notes are currently being processed
 const notesInProcess = new Set<string>();
 
+interface FailedItemRow {
+    noteId: string;
+    operation: string;
+    attempts: number;
+    lastAttempt: string;
+    error: string | null;
+    failed: number;
+}
+
+interface FailedItemWithTitle extends FailedItemRow {
+    title?: string;
+    failureType: 'chunks' | 'full';
+    isPermanent: boolean;
+}
+
 /**
  * Queues a note for embedding update
  */
@@ -77,17 +92,17 @@ export async function queueNoteForEmbedding(noteId: string, operation = 'UPDATE'
  */
 export async function getFailedEmbeddingNotes(limit: number = 100): Promise<any[]> {
     // Get notes with failed embedding attempts or permanently failed flag
-    const failedQueueItems = await sql.getRows(`
+    const failedQueueItems = sql.getRows<FailedItemRow>(`
         SELECT noteId, operation, attempts, lastAttempt, error, failed
         FROM embedding_queue
         WHERE attempts > 0 OR failed = 1
         ORDER BY failed DESC, attempts DESC, lastAttempt DESC
         LIMIT ?`,
         [limit]
-    ) as {noteId: string, operation: string, attempts: number, lastAttempt: string, error: string, failed: number}[];
+    );
 
     // Add titles to the failed notes
-    const failedNotesWithTitles = [];
+    const failedNotesWithTitles: FailedItemWithTitle[] = [];
     for (const item of failedQueueItems) {
         const note = becca.getNote(item.noteId);
         if (note) {
diff --git a/apps/server/src/services/llm/pipeline/stages/model_selection_stage.ts b/apps/server/src/services/llm/pipeline/stages/model_selection_stage.ts
index 35634c210..e5406997d 100644
--- a/apps/server/src/services/llm/pipeline/stages/model_selection_stage.ts
+++ b/apps/server/src/services/llm/pipeline/stages/model_selection_stage.ts
@@ -95,7 +95,7 @@ export class ModelSelectionStage extends BasePipelineStage<ModelSelectionInput,
             const providerPrecedence = await options.getOption('aiProviderPrecedence');
             if (providerPrecedence) {
                 // Parse provider precedence list
-                let providers = [];
+                let providers: string[] = [];
                 if (providerPrecedence.includes(',')) {
                     providers = providerPrecedence.split(',').map(p => p.trim());
                 } else if (providerPrecedence.startsWith('[') && providerPrecedence.endsWith(']')) {
diff --git a/apps/server/src/services/search/expressions/note_flat_text.ts b/apps/server/src/services/search/expressions/note_flat_text.ts
index 163dd38a0..1f4d4d87a 100644
--- a/apps/server/src/services/search/expressions/note_flat_text.ts
+++ b/apps/server/src/services/search/expressions/note_flat_text.ts
@@ -52,7 +52,7 @@ class NoteFlatTextExp extends Expression {
                 return;
             }
 
-            const foundAttrTokens = [];
+            const foundAttrTokens: string[] = [];
 
             for (const token of remainingTokens) {
                 if (note.type.includes(token) || note.mime.includes(token)) {
@@ -73,7 +73,7 @@ class NoteFlatTextExp extends Expression {
 
             for (const parentNote of note.parents) {
                 const title = normalize(beccaService.getNoteTitle(note.noteId, parentNote.noteId));
-                const foundTokens = foundAttrTokens.slice();
+                const foundTokens: string[] = foundAttrTokens.slice();
 
                 for (const token of remainingTokens) {
                     if (title.includes(token)) {
@@ -100,7 +100,7 @@ class NoteFlatTextExp extends Expression {
                 continue;
             }
 
-            const foundAttrTokens = [];
+            const foundAttrTokens: string[] = [];
 
             for (const token of this.tokens) {
                 if (note.type.includes(token) || note.mime.includes(token)) {
@@ -153,7 +153,7 @@ class NoteFlatTextExp extends Expression {
      * Returns noteIds which have at least one matching tokens
      */
     getCandidateNotes(noteSet: NoteSet): BNote[] {
-        const candidateNotes = [];
+        const candidateNotes: BNote[] = [];
 
         for (const note of noteSet.notes) {
             for (const token of this.tokens) {
diff --git a/packages/commons/src/lib/rows.ts b/packages/commons/src/lib/rows.ts
index 6b7d73a7e..735146eeb 100644
--- a/packages/commons/src/lib/rows.ts
+++ b/packages/commons/src/lib/rows.ts
@@ -126,17 +126,17 @@ export type NoteType = (typeof ALLOWED_NOTE_TYPES)[number];
 
 export interface NoteRow {
     noteId: string;
-    deleteId: string;
+    deleteId?: string;
     title: string;
     type: NoteType;
     mime: string;
-    isProtected: boolean;
-    isDeleted: boolean;
-    blobId: string;
-    dateCreated: string;
-    dateModified: string;
-    utcDateCreated: string;
-    utcDateModified: string;
+    isProtected?: boolean;
+    isDeleted?: boolean;
+    blobId?: string;
+    dateCreated?: string;
+    dateModified?: string;
+    utcDateCreated?: string;
+    utcDateModified?: string;
     content?: string | Buffer;
 }