chore: bump version to 0.5.2

- Fix pin icons in ConversationItem to use bookmark style matching TopNav
- Make pin() and archive() methods async with IndexedDB persistence
- Use optimistic updates with rollback on failure
- Queue changes for backend sync via markForSync()

README.md

@@ -41,20 +41,35 @@ If you want a **small, focused UI for local Ollama usage** → Vessel is built f
 ## Features
 
 ### Chat
-- Real-time streaming responses
-- Message editing with branch navigation
+- Real-time streaming responses with token metrics
+- **Message branching** — edit any message to create alternative conversation paths
 - Markdown rendering with syntax highlighting
+- **Thinking mode** — native support for reasoning models (DeepSeek-R1, etc.)
 - Dark/Light themes
 
+### Projects & Organization
+- **Projects** — group related conversations together
+- Pin and archive conversations
+- Smart title generation from conversation content
+- **Global search** — semantic, title, and content search across all chats
+
+### Knowledge Base (RAG)
+- Upload documents (text, markdown, PDF) to build a knowledge base
+- **Semantic search** using embeddings for context-aware retrieval
+- Project-specific or global knowledge bases
+- Automatic context injection into conversations
+
 ### Tools
 - **5 built-in tools**: web search, URL fetching, calculator, location, time
 - **Custom tools**: Create your own in JavaScript, Python, or HTTP
+- Agentic tool calling with chain-of-thought reasoning
 - Test tools before saving with the built-in testing panel
 
 ### Models
 - Browse and pull models from ollama.com
 - Create custom models with embedded system prompts
-- Track model updates
+- **Per-model parameters** — customize temperature, context size, top_k/top_p
+- Track model updates and capability detection (vision, tools, code)
 
 ### Prompts
 - Save and organize system prompts
@@ -145,6 +160,9 @@ Full documentation is available on the **[GitHub Wiki](https://github.com/Viking
 | Guide | Description |
 |-------|-------------|
 | [Getting Started](https://github.com/VikingOwl91/vessel/wiki/Getting-Started) | Installation and configuration |
+| [Projects](https://github.com/VikingOwl91/vessel/wiki/Projects) | Organize conversations into projects |
+| [Knowledge Base](https://github.com/VikingOwl91/vessel/wiki/Knowledge-Base) | RAG with document upload and semantic search |
+| [Search](https://github.com/VikingOwl91/vessel/wiki/Search) | Semantic and content search across chats |
 | [Custom Tools](https://github.com/VikingOwl91/vessel/wiki/Custom-Tools) | Create JavaScript, Python, or HTTP tools |
 | [System Prompts](https://github.com/VikingOwl91/vessel/wiki/System-Prompts) | Manage prompts with model defaults |
 | [Custom Models](https://github.com/VikingOwl91/vessel/wiki/Custom-Models) | Create models with embedded prompts |
@@ -164,6 +182,11 @@ Vessel prioritizes **usability and simplicity** over feature breadth.
 - [x] Custom tools (JavaScript, Python, HTTP)
 - [x] System prompt library with model-specific defaults
 - [x] Custom model creation with embedded prompts
+- [x] Projects for conversation organization
+- [x] Knowledge base with RAG (semantic retrieval)
+- [x] Global search (semantic, title, content)
+- [x] Thinking mode for reasoning models
+- [x] Message branching and conversation trees
 
 **Planned:**
 - [ ] Keyboard-first workflows

backend/cmd/server/main.go

@@ -18,7 +18,7 @@ import (
 )
 
 // Version is set at build time via -ldflags, or defaults to dev
-var Version = "0.5.0"
+var Version = "0.5.2"
 
 func getEnvOrDefault(key, defaultValue string) string {
 	if value := os.Getenv(key); value != "" {

frontend/package.json

@@ -1,6 +1,6 @@
 {
   "name": "vessel",
-  "version": "0.5.0",
+  "version": "0.5.2",
   "private": true,
   "type": "module",
   "scripts": {

frontend/src/lib/components/layout/ConversationItem.svelte

@@ -98,14 +98,18 @@
 	<!-- Chat icon -->
 	<div class="mt-0.5 shrink-0">
 		{#if conversation.isPinned}
-			<!-- Pin icon for pinned conversations -->
+			<!-- Bookmark icon for pinned conversations -->
 			<svg
 				xmlns="http://www.w3.org/2000/svg"
 				class="h-4 w-4 text-emerald-500"
-				viewBox="0 0 20 20"
+				viewBox="0 0 24 24"
 				fill="currentColor"
 			>
-				<path d="M10.75 4.75a.75.75 0 0 0-1.5 0v4.5h-4.5a.75.75 0 0 0 0 1.5h4.5v4.5a.75.75 0 0 0 1.5 0v-4.5h4.5a.75.75 0 0 0 0-1.5h-4.5v-4.5Z" />
+				<path
+					fill-rule="evenodd"
+					d="M6.32 2.577a49.255 49.255 0 0 1 11.36 0c1.497.174 2.57 1.46 2.57 2.93V21a.75.75 0 0 1-1.085.67L12 18.089l-7.165 3.583A.75.75 0 0 1 3.75 21V5.507c0-1.47 1.073-2.756 2.57-2.93Z"
+					clip-rule="evenodd"
+				/>
 			</svg>
 		{:else}
 			<!-- Regular chat bubble -->
@@ -147,49 +151,36 @@
 	</div>
 
 	<!-- Action buttons (always visible on mobile, hover on desktop) -->
-	<div class="absolute right-2 top-1/2 flex -translate-y-1/2 items-center gap-1 transition-opacity {uiState.isMobile ? 'opacity-100' : 'opacity-0 group-hover:opacity-100'}">
+	<div class="absolute right-2 top-1/2 flex -translate-y-1/2 items-center gap-0.5 rounded-md bg-theme-secondary/90 px-1 py-0.5 shadow-sm transition-opacity {uiState.isMobile ? 'opacity-100' : 'opacity-0 group-hover:opacity-100'}">
 		<!-- Pin/Unpin button -->
 		<button
 			type="button"
 			onclick={handlePin}
-			class="rounded p-1 text-theme-muted transition-colors hover:bg-theme-tertiary hover:text-theme-primary"
+			class="rounded p-1 transition-colors hover:bg-theme-tertiary {conversation.isPinned ? 'text-emerald-500 hover:text-emerald-400' : 'text-theme-secondary hover:text-theme-primary'}"
 			aria-label={conversation.isPinned ? 'Unpin conversation' : 'Pin conversation'}
 			title={conversation.isPinned ? 'Unpin' : 'Pin'}
 		>
-			{#if conversation.isPinned}
-				<!-- Unpin icon (filled) -->
-				<svg
-					xmlns="http://www.w3.org/2000/svg"
-					class="h-4 w-4"
-					viewBox="0 0 20 20"
-					fill="currentColor"
-				>
-					<path d="M8.75 10.25a.75.75 0 0 0 0 1.5h2.5a.75.75 0 0 0 0-1.5h-2.5Z" />
-				</svg>
-			{:else}
-				<!-- Pin icon (outline) -->
-				<svg
-					xmlns="http://www.w3.org/2000/svg"
-					class="h-4 w-4"
-					fill="none"
-					viewBox="0 0 24 24"
-					stroke="currentColor"
-					stroke-width="2"
-				>
-					<path
-						stroke-linecap="round"
-						stroke-linejoin="round"
-						d="M3 6.75A.75.75 0 0 1 3.75 6h16.5a.75.75 0 0 1 0 1.5H3.75A.75.75 0 0 1 3 6.75ZM3 12a.75.75 0 0 1 .75-.75h16.5a.75.75 0 0 1 0 1.5H3.75A.75.75 0 0 1 3 12Zm0 5.25a.75.75 0 0 1 .75-.75h16.5a.75.75 0 0 1 0 1.5H3.75a.75.75 0 0 1-.75-.75Z"
-					/>
-				</svg>
-			{/if}
+			<svg
+				xmlns="http://www.w3.org/2000/svg"
+				class="h-4 w-4"
+				fill={conversation.isPinned ? 'currentColor' : 'none'}
+				viewBox="0 0 24 24"
+				stroke="currentColor"
+				stroke-width="1.5"
+			>
+				<path
+					stroke-linecap="round"
+					stroke-linejoin="round"
+					d="M17.593 3.322c1.1.128 1.907 1.077 1.907 2.185V21L12 17.25 4.5 21V5.507c0-1.108.806-2.057 1.907-2.185a48.507 48.507 0 0 1 11.186 0Z"
+				/>
+			</svg>
 		</button>
 
 		<!-- Move to project button -->
 		<button
 			type="button"
 			onclick={handleMove}
-			class="rounded p-1 text-theme-muted transition-colors hover:bg-theme-tertiary hover:text-theme-primary"
+			class="rounded p-1 text-theme-secondary transition-colors hover:bg-theme-tertiary hover:text-theme-primary"
 			aria-label="Move to project"
 			title="Move to project"
 		>
@@ -213,7 +204,7 @@
 		<button
 			type="button"
 			onclick={handleExport}
-			class="rounded p-1 text-theme-muted transition-colors hover:bg-theme-tertiary hover:text-theme-primary"
+			class="rounded p-1 text-theme-secondary transition-colors hover:bg-theme-tertiary hover:text-theme-primary"
 			aria-label="Export conversation"
 			title="Export"
 		>
@@ -237,7 +228,7 @@
 		<button
 			type="button"
 			onclick={handleDelete}
-			class="rounded p-1 text-theme-muted transition-colors hover:bg-red-900/50 hover:text-red-400"
+			class="rounded p-1 text-theme-secondary transition-colors hover:bg-red-900/50 hover:text-red-400"
 			aria-label="Delete conversation"
 			title="Delete"
 		>

frontend/src/lib/components/layout/ProjectFolder.svelte

@@ -98,7 +98,7 @@
 		<button
 			type="button"
 			onclick={handleSettings}
-			class="shrink-0 rounded p-0.5 text-theme-muted opacity-0 transition-opacity hover:bg-theme-tertiary hover:text-theme-primary group-hover:opacity-100"
+			class="shrink-0 rounded p-1 text-theme-secondary opacity-0 transition-opacity hover:bg-theme-tertiary hover:text-theme-primary group-hover:opacity-100"
 			aria-label="Project settings"
 			title="Settings"
 		>

frontend/src/lib/components/projects/ProjectModal.svelte

@@ -5,6 +5,7 @@
 	import { projectsState, toastState } from '$lib/stores';
 	import type { Project } from '$lib/stores/projects.svelte.js';
 	import { addProjectLink, deleteProjectLink, getProjectLinks, type ProjectLink } from '$lib/storage/projects.js';
+	import { ConfirmDialog } from '$lib/components/shared';
 
 	interface Props {
 		isOpen: boolean;
@@ -26,6 +27,7 @@
 	let newLinkDescription = $state('');
 	let isLoading = $state(false);
 	let activeTab = $state<'settings' | 'instructions' | 'links'>('settings');
+	let showDeleteConfirm = $state(false);
 
 	// Predefined colors for quick selection
 	const presetColors = [
@@ -121,13 +123,14 @@
 		}
 	}
 
-	async function handleDelete() {
+	function handleDeleteClick() {
 		if (!projectId) return;
+		showDeleteConfirm = true;
+	}
 
-		if (!confirm('Delete this project? Conversations will be unlinked but not deleted.')) {
-			return;
-		}
-
+	async function handleDeleteConfirm() {
+		if (!projectId) return;
+		showDeleteConfirm = false;
 		isLoading = true;
 
 		try {
@@ -429,7 +432,7 @@
 					{#if projectId}
 						<button
 							type="button"
-							onclick={handleDelete}
+							onclick={handleDeleteClick}
 							disabled={isLoading}
 							class="rounded-lg px-4 py-2 text-sm font-medium text-red-500 transition-colors hover:bg-red-900/30 disabled:opacity-50"
 						>
@@ -458,3 +461,13 @@
 		</div>
 	</div>
 {/if}
+
+<ConfirmDialog
+	isOpen={showDeleteConfirm}
+	title="Delete Project"
+	message="Delete this project? Conversations will be unlinked but not deleted."
+	confirmText="Delete"
+	variant="danger"
+	onConfirm={handleDeleteConfirm}
+	onCancel={() => (showDeleteConfirm = false)}
+/>

frontend/src/lib/components/settings/KnowledgeTab.svelte

@@ -14,6 +14,7 @@
 	} from '$lib/memory';
 	import type { StoredDocument } from '$lib/storage/db';
 	import { toastState, modelsState } from '$lib/stores';
+	import { ConfirmDialog } from '$lib/components/shared';
 
 	let documents = $state<StoredDocument[]>([]);
 	let stats = $state({ documentCount: 0, chunkCount: 0, totalTokens: 0 });
@@ -22,6 +23,7 @@
 	let uploadProgress = $state({ current: 0, total: 0 });
 	let selectedModel = $state(DEFAULT_EMBEDDING_MODEL);
 	let dragOver = $state(false);
+	let deleteConfirm = $state<{ show: boolean; doc: StoredDocument | null }>({ show: false, doc: null });
 
 	let fileInput: HTMLInputElement;
 
@@ -90,10 +92,14 @@
 		uploadProgress = { current: 0, total: 0 };
 	}
 
-	async function handleDelete(doc: StoredDocument) {
-		if (!confirm(`Delete "${doc.name}"? This cannot be undone.`)) {
-			return;
-		}
+	function handleDeleteClick(doc: StoredDocument) {
+		deleteConfirm = { show: true, doc };
+	}
+
+	async function confirmDelete() {
+		if (!deleteConfirm.doc) return;
+		const doc = deleteConfirm.doc;
+		deleteConfirm = { show: false, doc: null };
 
 		try {
 			await deleteDocument(doc.id);
@@ -232,7 +238,7 @@
 
 						<button
 							type="button"
-							onclick={() => handleDelete(doc)}
+							onclick={() => handleDeleteClick(doc)}
 							class="rounded p-2 text-theme-muted transition-colors hover:bg-red-900/30 hover:text-red-400"
 							aria-label="Delete document"
 						>
@@ -273,3 +279,13 @@
 		{/if}
 	</section>
 </div>
+
+<ConfirmDialog
+	isOpen={deleteConfirm.show}
+	title="Delete Document"
+	message={`Delete "${deleteConfirm.doc?.name}"? This cannot be undone.`}
+	confirmText="Delete"
+	variant="danger"
+	onConfirm={confirmDelete}
+	onCancel={() => (deleteConfirm = { show: false, doc: null })}
+/>

frontend/src/lib/components/settings/PromptsTab.svelte

@@ -10,9 +10,11 @@
 		type PromptTemplate,
 		type PromptCategory
 	} from '$lib/prompts/templates';
+	import { ConfirmDialog } from '$lib/components/shared';
 
 	type Tab = 'my-prompts' | 'browse-templates';
 	let activeTab = $state<Tab>('my-prompts');
+	let deleteConfirm = $state<{ show: boolean; prompt: Prompt | null }>({ show: false, prompt: null });
 
 	let showEditor = $state(false);
 	let editingPrompt = $state<Prompt | null>(null);
@@ -106,10 +108,14 @@
 		}
 	}
 
-	async function handleDelete(prompt: Prompt): Promise<void> {
-		if (confirm(`Delete "${prompt.name}"? This cannot be undone.`)) {
-			await promptsState.remove(prompt.id);
-		}
+	function handleDeleteClick(prompt: Prompt): void {
+		deleteConfirm = { show: true, prompt };
+	}
+
+	async function confirmDelete(): Promise<void> {
+		if (!deleteConfirm.prompt) return;
+		await promptsState.remove(deleteConfirm.prompt.id);
+		deleteConfirm = { show: false, prompt: null };
 	}
 
 	async function handleSetDefault(prompt: Prompt): Promise<void> {
@@ -286,7 +292,7 @@
 										<path stroke-linecap="round" stroke-linejoin="round" d="M11 5H6a2 2 0 00-2 2v11a2 2 0 002 2h11a2 2 0 002-2v-5m-1.414-9.414a2 2 0 112.828 2.828L11.828 15H9v-2.828l8.586-8.586z" />
 									</svg>
 								</button>
-								<button type="button" onclick={() => handleDelete(prompt)} class="rounded p-1.5 text-theme-muted hover:bg-red-900/30 hover:text-red-400" title="Delete">
+								<button type="button" onclick={() => handleDeleteClick(prompt)} class="rounded p-1.5 text-theme-muted hover:bg-red-900/30 hover:text-red-400" title="Delete">
 									<svg xmlns="http://www.w3.org/2000/svg" class="h-4 w-4" fill="none" viewBox="0 0 24 24" stroke="currentColor" stroke-width="2">
 										<path stroke-linecap="round" stroke-linejoin="round" d="M19 7l-.867 12.142A2 2 0 0116.138 21H7.862a2 2 0 01-1.995-1.858L5 7m5 4v6m4-6v6m1-10V4a1 1 0 00-1-1h-4a1 1 0 00-1 1v3M4 7h16" />
 									</svg>
@@ -444,3 +450,13 @@
 		</div>
 	</div>
 {/if}
+
+<ConfirmDialog
+	isOpen={deleteConfirm.show}
+	title="Delete Prompt"
+	message={`Delete "${deleteConfirm.prompt?.name}"? This cannot be undone.`}
+	confirmText="Delete"
+	variant="danger"
+	onConfirm={confirmDelete}
+	onCancel={() => (deleteConfirm = { show: false, prompt: null })}
+/>

frontend/src/lib/components/settings/ToolsTab.svelte

@@ -5,11 +5,13 @@
 	import { toolsState } from '$lib/stores';
 	import type { ToolDefinition, CustomTool } from '$lib/tools';
 	import { ToolEditor } from '$lib/components/tools';
+	import { ConfirmDialog } from '$lib/components/shared';
 
 	let showEditor = $state(false);
 	let editingTool = $state<CustomTool | null>(null);
 	let searchQuery = $state('');
 	let expandedDescriptions = $state<Set<string>>(new Set());
+	let deleteConfirm = $state<{ show: boolean; tool: CustomTool | null }>({ show: false, tool: null });
 
 	function openCreateEditor(): void {
 		editingTool = null;
@@ -32,9 +34,14 @@
 	}
 
 	function handleDeleteTool(tool: CustomTool): void {
-		if (confirm(`Delete "${tool.name}"? This cannot be undone.`)) {
-			toolsState.removeCustomTool(tool.id);
+		deleteConfirm = { show: true, tool };
+	}
+
+	function confirmDeleteTool(): void {
+		if (deleteConfirm.tool) {
+			toolsState.removeCustomTool(deleteConfirm.tool.id);
 		}
+		deleteConfirm = { show: false, tool: null };
 	}
 
 	const allTools = $derived(toolsState.getAllToolsWithState());
@@ -509,3 +516,13 @@
 	onClose={() => { showEditor = false; editingTool = null; }}
 	onSave={handleSaveTool}
 />
+
+<ConfirmDialog
+	isOpen={deleteConfirm.show}
+	title="Delete Tool"
+	message={`Delete "${deleteConfirm.tool?.name}"? This cannot be undone.`}
+	confirmText="Delete"
+	variant="danger"
+	onConfirm={confirmDeleteTool}
+	onCancel={() => (deleteConfirm = { show: false, tool: null })}
+/>

frontend/src/lib/storage/projects.ts

@@ -175,7 +175,7 @@ export async function updateProject(
  */
 export async function deleteProject(id: string): Promise<StorageResult<void>> {
 	return withErrorHandling(async () => {
-		await db.transaction('rw', [db.projects, db.projectLinks, db.conversations, db.documents, db.chatChunks], async () => {
+		await db.transaction('rw', [db.projects, db.projectLinks, db.conversations, db.documents, db.chunks, db.chatChunks], async () => {
 			// Unlink all conversations from this project
 			const conversations = await db.conversations.where('projectId').equals(id).toArray();
 			for (const conv of conversations) {

frontend/src/lib/stores/conversations.svelte.ts

@@ -4,6 +4,7 @@
  */
 
 import type { Conversation } from '$lib/types/conversation.js';
+import { pinConversation, archiveConversation } from '$lib/storage/conversations.js';
 
 /** Date group labels */
 type DateGroup = 'Today' | 'Yesterday' | 'Previous 7 Days' | 'Previous 30 Days' | 'Older';
@@ -161,23 +162,43 @@ export class ConversationsState {
 
 	/**
 	 * Toggle pin status of a conversation
+	 * Persists to IndexedDB and queues for backend sync
 	 * @param id The conversation ID
 	 */
-	pin(id: string): void {
+	async pin(id: string): Promise<void> {
 		const conversation = this.items.find((c) => c.id === id);
 		if (conversation) {
+			// Update in-memory state immediately for responsive UI
 			this.update(id, { isPinned: !conversation.isPinned });
+
+			// Persist to IndexedDB and queue for sync
+			const result = await pinConversation(id);
+			if (!result.success) {
+				// Revert on failure
+				this.update(id, { isPinned: conversation.isPinned });
+				console.error('Failed to persist pin state:', result.error);
+			}
 		}
 	}
 
 	/**
 	 * Toggle archive status of a conversation
+	 * Persists to IndexedDB and queues for backend sync
 	 * @param id The conversation ID
 	 */
-	archive(id: string): void {
+	async archive(id: string): Promise<void> {
 		const conversation = this.items.find((c) => c.id === id);
 		if (conversation) {
+			// Update in-memory state immediately for responsive UI
 			this.update(id, { isArchived: !conversation.isArchived });
+
+			// Persist to IndexedDB and queue for sync
+			const result = await archiveConversation(id);
+			if (!result.success) {
+				// Revert on failure
+				this.update(id, { isArchived: conversation.isArchived });
+				console.error('Failed to persist archive state:', result.error);
+			}
 		}
 	}
 

frontend/src/routes/projects/[id]/+page.svelte

@@ -20,6 +20,7 @@
 	import type { StoredDocument } from '$lib/storage/db';
 	import ProjectModal from '$lib/components/projects/ProjectModal.svelte';
 	import { searchProjectChatHistory, type ChatSearchResult } from '$lib/services/chat-indexer.js';
+	import { ConfirmDialog } from '$lib/components/shared';
 
 	// Get project ID from URL
 	const projectId = $derived($page.params.id);
@@ -50,6 +51,7 @@
 	let isSearching = $state(false);
 	let searchResults = $state<ChatSearchResult[]>([]);
 	let searchDebounceTimer: ReturnType<typeof setTimeout> | null = null;
+	let deleteDocConfirm = $state<{ show: boolean; doc: StoredDocument | null }>({ show: false, doc: null });
 
 	// Map of conversationId -> best matching snippet from search
 	const searchSnippetMap = $derived.by(() => {
@@ -323,8 +325,14 @@
 		await loadProjectData();
 	}
 
-	async function handleDeleteDocument(doc: StoredDocument) {
-		if (!confirm(`Delete "${doc.name}"? This cannot be undone.`)) return;
+	function handleDeleteDocumentClick(doc: StoredDocument) {
+		deleteDocConfirm = { show: true, doc };
+	}
+
+	async function confirmDeleteDocument() {
+		if (!deleteDocConfirm.doc) return;
+		const doc = deleteDocConfirm.doc;
+		deleteDocConfirm = { show: false, doc: null };
 
 		try {
 			await deleteDocument(doc.id);
@@ -632,7 +640,7 @@
 									</div>
 									<button
 										type="button"
-										onclick={() => handleDeleteDocument(doc)}
+										onclick={() => handleDeleteDocumentClick(doc)}
 										class="rounded p-1.5 text-theme-muted transition-colors hover:bg-red-900/30 hover:text-red-400"
 									>
 										<svg xmlns="http://www.w3.org/2000/svg" class="h-4 w-4" fill="none" viewBox="0 0 24 24" stroke="currentColor" stroke-width="2">
@@ -705,3 +713,14 @@
 	{projectId}
 	onUpdate={() => loadProjectData()}
 />
+
+<!-- Delete Document Confirm -->
+<ConfirmDialog
+	isOpen={deleteDocConfirm.show}
+	title="Delete Document"
+	message={`Delete "${deleteDocConfirm.doc?.name}"? This cannot be undone.`}
+	confirmText="Delete"
+	variant="danger"
+	onConfirm={confirmDeleteDocument}
+	onCancel={() => (deleteDocConfirm = { show: false, doc: null })}
+/>