diff --git a/apps/server/src/services/i18n.ts b/apps/server/src/services/i18n.ts
index 3bdf6f9cd..3e1f4d1a6 100644
--- a/apps/server/src/services/i18n.ts
+++ b/apps/server/src/services/i18n.ts
@@ -51,7 +51,7 @@ export function getLocales(): Locale[] {
 }
 
 function getCurrentLanguage(): LOCALE_IDS {
-    let language: string;
+    let language: string | null = null;
     if (sql_init.isDbInitialized()) {
         language = options.getOptionOrNull("locale");
     }
diff --git a/apps/server/src/services/import/opml.ts b/apps/server/src/services/import/opml.ts
index cdc01011f..934578c70 100644
--- a/apps/server/src/services/import/opml.ts
+++ b/apps/server/src/services/import/opml.ts
@@ -84,7 +84,7 @@ async function importOpml(taskContext: TaskContext, fileBuffer: string | Buffer,
     }
 
     const outlines = xml.opml.body[0].outline || [];
-    let returnNote = null;
+    let returnNote: BNote | null = null;
 
     for (const outline of outlines) {
         const note = importOutline(outline, parentNote.noteId);
diff --git a/apps/server/src/services/llm/ai_interface.ts b/apps/server/src/services/llm/ai_interface.ts
index b8349b5b2..df8cc6914 100644
--- a/apps/server/src/services/llm/ai_interface.ts
+++ b/apps/server/src/services/llm/ai_interface.ts
@@ -9,7 +9,7 @@ export interface Message {
     content: string;
     name?: string;
     tool_call_id?: string;
-    tool_calls?: ToolCall[];
+    tool_calls?: ToolCall[] | null;
     sessionId?: string; // Optional session ID for WebSocket communication
 }
 
@@ -210,7 +210,7 @@ export interface ChatResponse {
     stream?: (callback: (chunk: StreamChunk) => Promise<void> | void) => Promise<string>;
 
     /** Tool calls from the LLM (if tools were used and the model supports them) */
-    tool_calls?: ToolCall[];
+    tool_calls?: ToolCall[] | null;
 }
 
 export interface AIService {
diff --git a/apps/server/src/services/llm/embeddings/embeddings_interface.ts b/apps/server/src/services/llm/embeddings/embeddings_interface.ts
index b1fa333bf..1db6c5099 100644
--- a/apps/server/src/services/llm/embeddings/embeddings_interface.ts
+++ b/apps/server/src/services/llm/embeddings/embeddings_interface.ts
@@ -22,20 +22,24 @@ export interface NoteEmbeddingContext {
         title: string;
         mime: string;
     }[];
-    backlinks?: {
-        sourceNoteId: string;
-        sourceTitle: string;
-        relationName: string;
-    }[];
-    relatedNotes?: {
-        targetNoteId: string;
-        targetTitle: string;
-        relationName: string;
-    }[];
+    backlinks?: Backlink[];
+    relatedNotes?: RelatedNote[];
     labelValues?: Record<string, string>;
     templateTitles?: string[];
 }
 
+export interface Backlink {
+    sourceNoteId: string;
+    sourceTitle: string;
+    relationName: string;
+}
+
+export interface RelatedNote {
+    targetNoteId: string;
+    targetTitle: string;
+    relationName: string;
+}
+
 /**
  * Information about an embedding model's capabilities
  */
diff --git a/apps/server/src/services/llm/embeddings/storage.ts b/apps/server/src/services/llm/embeddings/storage.ts
index 67063e63b..675047a76 100644
--- a/apps/server/src/services/llm/embeddings/storage.ts
+++ b/apps/server/src/services/llm/embeddings/storage.ts
@@ -8,6 +8,14 @@ import entityChangesService from "../../../services/entity_changes.js";
 import type { EntityChange } from "../../../services/entity_changes_interface.js";
 import { EMBEDDING_CONSTANTS } from "../constants/embedding_constants.js";
 import { SEARCH_CONSTANTS } from '../constants/search_constants.js';
+
+interface Similarity {
+    noteId: string;
+    similarity: number;
+    contentType: string;
+    bonuses?: Record<string, number>; // Optional for debugging
+}
+
 /**
  * Creates or updates an embedding for a note
  */
@@ -434,7 +442,7 @@ async function processEmbeddings(queryEmbedding: Float32Array, embeddings: any[]
         return { bonuses, totalBonus };
     }
 
-    const similarities = [];
+    const similarities: Similarity[] = [];
 
     try {
         // Try to extract the original query text if it was added to the metadata
diff --git a/apps/server/src/services/llm/providers/anthropic_service.ts b/apps/server/src/services/llm/providers/anthropic_service.ts
index 955ef494a..cbdbb6814 100644
--- a/apps/server/src/services/llm/providers/anthropic_service.ts
+++ b/apps/server/src/services/llm/providers/anthropic_service.ts
@@ -7,6 +7,21 @@ import { getAnthropicOptions } from './providers.js';
 import log from '../../log.js';
 import Anthropic from '@anthropic-ai/sdk';
 import { SEARCH_CONSTANTS } from '../constants/search_constants.js';
+import type { ToolCall } from '../tools/tool_interfaces.js';
+
+interface AnthropicMessage extends Omit<Message, "content"> {
+    content: MessageContent[] | string;
+}
+
+interface MessageContent {
+    type: "text" | "tool_use" | "tool_result";
+    text?: string;
+    id?: string;
+    name?: string;
+    content?: string;
+    tool_use_id?: string;
+    input?: string | Record<string, unknown>;
+}
 
 export class AnthropicService extends BaseAIService {
     private client: any = null;
@@ -130,7 +145,7 @@ export class AnthropicService extends BaseAIService {
                     .join('');
 
                 // Process tool calls if any are present in the response
-                let toolCalls = null;
+                let toolCalls: ToolCall[] | null = null;
                 if (response.content) {
                     const toolBlocks = response.content.filter((block: any) =>
                         block.type === 'tool_use' ||
@@ -157,7 +172,7 @@ export class AnthropicService extends BaseAIService {
                             return null;
                         }).filter(Boolean);
 
-                        log.info(`Extracted ${toolCalls.length} tool calls from Anthropic response`);
+                        log.info(`Extracted ${toolCalls?.length} tool calls from Anthropic response`);
                     }
                 }
 
@@ -406,8 +421,8 @@ export class AnthropicService extends BaseAIService {
     /**
      * Format messages for the Anthropic API
      */
-    private formatMessages(messages: Message[]): any[] {
-        const anthropicMessages: any[] = [];
+    private formatMessages(messages: Message[]): AnthropicMessage[] {
+        const anthropicMessages: AnthropicMessage[] = [];
 
         // Process each message
         for (const msg of messages) {
@@ -424,7 +439,7 @@ export class AnthropicService extends BaseAIService {
                 // Assistant messages need special handling for tool_calls
                 if (msg.tool_calls && msg.tool_calls.length > 0) {
                     // Create content blocks array for tool calls
-                    const content = [];
+                    const content: MessageContent[] = [];
 
                     // Add text content if present
                     if (msg.content) {
diff --git a/apps/server/src/services/llm/providers/providers.ts b/apps/server/src/services/llm/providers/providers.ts
index 5fcd4286a..91295ffe0 100644
--- a/apps/server/src/services/llm/providers/providers.ts
+++ b/apps/server/src/services/llm/providers/providers.ts
@@ -181,7 +181,7 @@ export async function updateEmbeddingProviderConfig(
     }
 
     // Build update query parts
-    const updates = [];
+    const updates: string[] = [];
     const params: any[] = [];
 
     if (priority !== undefined) {
diff --git a/apps/server/src/services/llm/tools/content_extraction_tool.ts b/apps/server/src/services/llm/tools/content_extraction_tool.ts
index 0a1a18cd7..52c1409e9 100644
--- a/apps/server/src/services/llm/tools/content_extraction_tool.ts
+++ b/apps/server/src/services/llm/tools/content_extraction_tool.ts
@@ -8,6 +8,26 @@ import type { Tool, ToolHandler } from './tool_interfaces.js';
 import log from '../../log.js';
 import becca from '../../../becca/becca.js';
 
+interface CodeBlock {
+    code: string;
+    language?: string;
+}
+
+interface Heading {
+    text: string;
+    level: number; // 1 for H1, 2 for H2, etc.
+}
+
+interface List {
+    type: "unordered" | "ordered";
+    items: string[];
+}
+
+interface Table {
+    headers: string[];
+    rows: string[][];
+}
+
 /**
  * Definition of the content extraction tool
  */
@@ -137,8 +157,8 @@ export class ContentExtractionTool implements ToolHandler {
     /**
      * Extract lists from HTML content
      */
-    private extractLists(content: string): Array<{ type: string, items: string[] }> {
-        const lists = [];
+    private extractLists(content: string): List[] {
+        const lists: List[] = [];
 
         // Extract unordered lists
         const ulRegex = /<ul[^>]*>([\s\S]*?)<\/ul>/gi;
@@ -179,7 +199,7 @@ export class ContentExtractionTool implements ToolHandler {
      * Extract list items from list content
      */
     private extractListItems(listContent: string): string[] {
-        const items = [];
+        const items: string[] = [];
         const itemRegex = /<li[^>]*>([\s\S]*?)<\/li>/gi;
         let itemMatch;
 
@@ -196,15 +216,15 @@ export class ContentExtractionTool implements ToolHandler {
     /**
      * Extract tables from HTML content
      */
-    private extractTables(content: string): Array<{ headers: string[], rows: string[][] }> {
-        const tables = [];
+    private extractTables(content: string): Table[] {
+        const tables: Table[] = [];
         const tableRegex = /<table[^>]*>([\s\S]*?)<\/table>/gi;
-        let tableMatch;
+        let tableMatch: RegExpExecArray | null;
 
         while ((tableMatch = tableRegex.exec(content)) !== null) {
             const tableContent = tableMatch[1];
-            const headers = [];
-            const rows = [];
+            const headers: string[] = [];
+            const rows: string[][] = [];
 
             // Extract table headers
             const headerRegex = /<th[^>]*>([\s\S]*?)<\/th>/gi;
@@ -218,7 +238,7 @@ export class ContentExtractionTool implements ToolHandler {
             let rowMatch;
             while ((rowMatch = rowRegex.exec(tableContent)) !== null) {
                 const rowContent = rowMatch[1];
-                const cells = [];
+                const cells: string[] = [];
 
                 const cellRegex = /<td[^>]*>([\s\S]*?)<\/td>/gi;
                 let cellMatch;
@@ -246,7 +266,7 @@ export class ContentExtractionTool implements ToolHandler {
      * Extract headings from HTML content
      */
     private extractHeadings(content: string): Array<{ level: number, text: string }> {
-        const headings = [];
+        const headings: Heading[] = [];
 
         for (let i = 1; i <= 6; i++) {
             const headingRegex = new RegExp(`<h${i}[^>]*>([\\s\\S]*?)<\/h${i}>`, 'gi');
@@ -270,7 +290,7 @@ export class ContentExtractionTool implements ToolHandler {
      * Extract code blocks from HTML content
      */
     private extractCodeBlocks(content: string): Array<{ language?: string, code: string }> {
-        const codeBlocks = [];
+        const codeBlocks: CodeBlock[] = [];
 
         // Look for <pre> and <code> blocks
         const preRegex = /<pre[^>]*>([\s\S]*?)<\/pre>/gi;
diff --git a/apps/server/src/services/llm/tools/note_creation_tool.ts b/apps/server/src/services/llm/tools/note_creation_tool.ts
index 9633880e4..41e608029 100644
--- a/apps/server/src/services/llm/tools/note_creation_tool.ts
+++ b/apps/server/src/services/llm/tools/note_creation_tool.ts
@@ -9,6 +9,7 @@ import log from '../../log.js';
 import becca from '../../../becca/becca.js';
 import notes from '../../notes.js';
 import attributes from '../../attributes.js';
+import type { BNote } from '../../backend_script_entrypoint.js';
 
 /**
  * Definition of the note creation tool
@@ -89,7 +90,7 @@ export class NoteCreationTool implements ToolHandler {
             log.info(`Executing create_note tool - Title: "${title}", Type: ${type}, ParentNoteId: ${parentNoteId || 'root'}`);
 
             // Validate parent note exists if specified
-            let parent = null;
+            let parent: BNote | null = null;
             if (parentNoteId) {
                 parent = becca.notes[parentNoteId];
                 if (!parent) {
diff --git a/apps/server/src/services/llm/tools/relationship_tool.ts b/apps/server/src/services/llm/tools/relationship_tool.ts
index 09e16f72c..a7023981d 100644
--- a/apps/server/src/services/llm/tools/relationship_tool.ts
+++ b/apps/server/src/services/llm/tools/relationship_tool.ts
@@ -10,6 +10,14 @@ import becca from '../../../becca/becca.js';
 import attributes from '../../attributes.js';
 import aiServiceManager from '../ai_service_manager.js';
 import { SEARCH_CONSTANTS } from '../constants/search_constants.js';
+import type { Backlink, RelatedNote } from '../embeddings/embeddings_interface.js';
+
+interface Suggestion {
+    targetNoteId: string;
+    targetTitle: string;
+    similarity: number;
+    suggestedRelation: string;
+}
 
 /**
  * Definition of the relationship tool
@@ -180,7 +188,7 @@ export class RelationshipTool implements ToolHandler {
                 .filter((attr: any) => attr.type === 'relation')
                 .slice(0, limit);
 
-            const outgoingRelations = [];
+            const outgoingRelations: RelatedNote[] = [];
 
             for (const attr of outgoingAttributes) {
                 const targetNote = becca.notes[attr.value];
@@ -196,7 +204,7 @@ export class RelationshipTool implements ToolHandler {
 
             // Get incoming relationships (where this note is the target)
             // Since becca.findNotesWithRelation doesn't exist, use attributes to find notes with relation
-            const incomingRelations = [];
+            const incomingRelations: Backlink[] = [];
 
             // Find all attributes of type relation that point to this note
             const relationAttributes = sourceNote.getTargetRelations();
@@ -321,7 +329,7 @@ export class RelationshipTool implements ToolHandler {
             const sourceContent = await sourceNote.getContent();
 
             // Prepare suggestions
-            const suggestions = [];
+            const suggestions: Suggestion[] = [];
 
             for (const relatedNote of relatedResult.relatedNotes) {
                 try {
diff --git a/apps/server/src/services/notes.ts b/apps/server/src/services/notes.ts
index cbb3c90c1..f06e07ed8 100644
--- a/apps/server/src/services/notes.ts
+++ b/apps/server/src/services/notes.ts
@@ -755,7 +755,7 @@ function updateNoteData(noteId: string, content: string, attachments: Attachment
 function undeleteNote(noteId: string, taskContext: TaskContext) {
     const noteRow = sql.getRow<NoteRow>("SELECT * FROM notes WHERE noteId = ?", [noteId]);
 
-    if (!noteRow.isDeleted) {
+    if (!noteRow.isDeleted || !noteRow.deleteId) {
         log.error(`Note '${noteId}' is not deleted and thus cannot be undeleted.`);
         return;
     }
diff --git a/apps/server/src/services/script.ts b/apps/server/src/services/script.ts
index aedab83bf..1afc3b763 100644
--- a/apps/server/src/services/script.ts
+++ b/apps/server/src/services/script.ts
@@ -118,7 +118,7 @@ function getParams(params?: ScriptParams) {
 }
 
 function getScriptBundleForFrontend(note: BNote, script?: string, params?: ScriptParams) {
-    let overrideContent = null;
+    let overrideContent: string | null = null;
 
     if (script) {
         overrideContent = `return (${script}\r\n)(${getParams(params)})`;
@@ -170,7 +170,7 @@ function getScriptBundle(note: BNote, root: boolean = true, scriptEnv: string |
 
     includedNoteIds.push(note.noteId);
 
-    const modules = [];
+    const modules: BNote[] = [];
 
     for (const child of note.getChildNotes()) {
         const childBundle = getScriptBundle(child, false, scriptEnv, includedNoteIds);
diff --git a/apps/server/src/services/search/services/parse.ts b/apps/server/src/services/search/services/parse.ts
index c454aef7e..6cfaad6e6 100644
--- a/apps/server/src/services/search/services/parse.ts
+++ b/apps/server/src/services/search/services/parse.ts
@@ -294,11 +294,11 @@ function getExpression(tokens: TokenData[], searchContext: SearchContext, level
             valueExtractor: ValueExtractor;
             direction: string;
         }[] = [];
-        let limit;
+        let limit: number | undefined = undefined;
 
         if (tokens[i].token === "orderby") {
             do {
-                const propertyPath = [];
+                const propertyPath: string[] = [];
                 let direction = "asc";
 
                 do {
diff --git a/apps/server/src/services/search/services/search.ts b/apps/server/src/services/search/services/search.ts
index 3e1020e7a..7c53546e7 100644
--- a/apps/server/src/services/search/services/search.ts
+++ b/apps/server/src/services/search/services/search.ts
@@ -36,7 +36,7 @@ function searchFromNote(note: BNote): SearchNoteResult {
 
     const searchScript = note.getRelationValue("searchScript");
     const searchString = note.getLabelValue("searchString") || "";
-    let error = null;
+    let error: string | null = null;
 
     if (searchScript) {
         searchResultNoteIds = searchFromRelation(note, "searchScript");
diff --git a/apps/server/src/share/shaca/shaca-interface.ts b/apps/server/src/share/shaca/shaca-interface.ts
index 65b0585b7..1d796b302 100644
--- a/apps/server/src/share/shaca/shaca-interface.ts
+++ b/apps/server/src/share/shaca/shaca-interface.ts
@@ -43,7 +43,7 @@ export default class Shaca {
     }
 
     getNotes(noteIds: string[], ignoreMissing = false) {
-        const filteredNotes = [];
+        const filteredNotes: SNote[] = [];
 
         for (const noteId of noteIds) {
             const note = this.notes[noteId];