diff --git a/src/content-selector.ts b/src/content-selector.ts
new file mode 100644
index 0000000..604276a
--- /dev/null
+++ b/src/content-selector.ts
@@ -0,0 +1,400 @@
+import { App, CachedMetadata, HeadingCache, SectionCache, TFile } from 'obsidian';
+import { estimateTokens } from './history';
+
+// === Types ===
+
+export interface HeadingNode {
+	heading: string;
+	level: number;
+	position: { start: number; end: number };
+	children: HeadingNode[];
+	selected: boolean;
+}
+
+export interface FileSelection {
+	file: TFile;
+	selected: boolean;
+	expanded: boolean;
+	headings: HeadingNode[];
+	blocks: BlockNode[];
+	fullContent: string;
+}
+
+export interface BlockNode {
+	id: string;
+	position: { start: number; end: number };
+	selected: boolean;
+}
+
+export interface ContentReference {
+	noteName: string;
+	headingPath: string[];
+	blockId: string | null;
+}
+
+// === Reference Syntax Parser ===
+
+/**
+ * Parse a reference string like "NoteName#Heading1#Heading2" or "NoteName^blockid"
+ */
+export function parseReference(ref: string): ContentReference {
+	const blockMatch = ref.match(/^(.+?)\^(\w+)$/);
+	if (blockMatch) {
+		return {
+			noteName: blockMatch[1] || '',
+			headingPath: [],
+			blockId: blockMatch[2] || null,
+		};
+	}
+
+	const parts = ref.split('#');
+	return {
+		noteName: parts[0] || '',
+		headingPath: parts.slice(1).filter(p => p),
+		blockId: null,
+	};
+}
+
+/**
+ * Format a reference back to string
+ */
+export function formatReference(ref: ContentReference): string {
+	if (ref.blockId) {
+		return `${ref.noteName}^${ref.blockId}`;
+	}
+	if (ref.headingPath.length > 0) {
+		return `${ref.noteName}#${ref.headingPath.join('#')}`;
+	}
+	return ref.noteName;
+}
+
+// === Content Selector ===
+
+export class ContentSelector {
+	private app: App;
+
+	constructor(app: App) {
+		this.app = app;
+	}
+
+	/**
+	 * Build a FileSelection with heading structure for a file
+	 */
+	async buildFileSelection(file: TFile): Promise<FileSelection> {
+		const content = await this.app.vault.read(file);
+		const cache = this.app.metadataCache.getFileCache(file);
+
+		const headings = this.buildHeadingTree(cache, content);
+		const blocks = this.extractBlocks(cache, content);
+
+		return {
+			file,
+			selected: true,
+			expanded: false,
+			headings,
+			blocks,
+			fullContent: content,
+		};
+	}
+
+	/**
+	 * Build hierarchical heading tree from cache
+	 */
+	private buildHeadingTree(cache: CachedMetadata | null, content: string): HeadingNode[] {
+		if (!cache?.headings || cache.headings.length === 0) {
+			return [];
+		}
+
+		const lines = content.split('\n');
+		const headings = cache.headings;
+		const root: HeadingNode[] = [];
+		const stack: { node: HeadingNode; level: number }[] = [];
+
+		for (let i = 0; i < headings.length; i++) {
+			const h = headings[i];
+			if (!h) continue;
+
+			// Calculate end position (start of next heading or end of file)
+			const nextHeading = headings[i + 1];
+			const endLine = nextHeading
+				? nextHeading.position.start.line - 1
+				: lines.length - 1;
+
+			const node: HeadingNode = {
+				heading: h.heading,
+				level: h.level,
+				position: {
+					start: h.position.start.offset,
+					end: this.getLineEndOffset(lines, endLine),
+				},
+				children: [],
+				selected: true,
+			};
+
+			// Find parent based on level
+			while (stack.length > 0) {
+				const last = stack[stack.length - 1];
+				if (last && last.level < h.level) {
+					break;
+				}
+				stack.pop();
+			}
+
+			if (stack.length === 0) {
+				root.push(node);
+			} else {
+				const parent = stack[stack.length - 1];
+				if (parent) {
+					parent.node.children.push(node);
+				}
+			}
+
+			stack.push({ node, level: h.level });
+		}
+
+		return root;
+	}
+
+	private getLineEndOffset(lines: string[], lineIndex: number): number {
+		let offset = 0;
+		for (let i = 0; i <= lineIndex && i < lines.length; i++) {
+			const line = lines[i];
+			offset += (line?.length || 0) + 1; // +1 for newline
+		}
+		return offset;
+	}
+
+	/**
+	 * Extract block references from cache
+	 */
+	private extractBlocks(cache: CachedMetadata | null, content: string): BlockNode[] {
+		if (!cache?.sections) {
+			return [];
+		}
+
+		const blocks: BlockNode[] = [];
+
+		for (const section of cache.sections) {
+			if (section.id) {
+				blocks.push({
+					id: section.id,
+					position: {
+						start: section.position.start.offset,
+						end: section.position.end.offset,
+					},
+					selected: true,
+				});
+			}
+		}
+
+		return blocks;
+	}
+
+	/**
+	 * Extract content based on selection
+	 */
+	extractSelectedContent(selection: FileSelection): string {
+		if (!selection.selected) {
+			return '';
+		}
+
+		// If no headings or all headings selected, return full content
+		if (selection.headings.length === 0 || this.allHeadingsSelected(selection.headings)) {
+			return selection.fullContent;
+		}
+
+		// Build content from selected headings
+		const parts: string[] = [];
+		this.collectSelectedContent(selection.headings, selection.fullContent, parts);
+
+		return parts.join('\n\n');
+	}
+
+	private allHeadingsSelected(headings: HeadingNode[]): boolean {
+		for (const h of headings) {
+			if (!h.selected) return false;
+			if (!this.allHeadingsSelected(h.children)) return false;
+		}
+		return true;
+	}
+
+	private collectSelectedContent(headings: HeadingNode[], fullContent: string, parts: string[]): void {
+		for (const h of headings) {
+			if (h.selected) {
+				// Include this heading and all its content
+				const content = fullContent.substring(h.position.start, h.position.end).trim();
+				if (content) {
+					parts.push(content);
+				}
+			} else {
+				// Not selected, but check children
+				this.collectSelectedContent(h.children, fullContent, parts);
+			}
+		}
+	}
+
+	/**
+	 * Extract content for a specific heading path
+	 */
+	extractByHeadingPath(content: string, cache: CachedMetadata | null, headingPath: string[]): string | null {
+		if (!cache?.headings || headingPath.length === 0) {
+			return null;
+		}
+
+		const lines = content.split('\n');
+		let currentLevel = 0;
+		let pathIndex = 0;
+		let startOffset: number | null = null;
+		let endOffset: number | null = null;
+
+		for (let i = 0; i < cache.headings.length; i++) {
+			const h = cache.headings[i];
+			if (!h) continue;
+
+			const targetHeading = headingPath[pathIndex];
+
+			if (startOffset !== null) {
+				// We're inside the target heading, look for end
+				if (h.level <= currentLevel) {
+					// Found a heading at same or higher level, this ends our section
+					endOffset = h.position.start.offset;
+					break;
+				}
+			} else {
+				// Looking for the target heading
+				if (h.heading.toLowerCase() === targetHeading?.toLowerCase()) {
+					if (pathIndex === headingPath.length - 1) {
+						// Found the final heading in the path
+						startOffset = h.position.start.offset;
+						currentLevel = h.level;
+					} else {
+						// Found an intermediate heading, continue looking
+						pathIndex++;
+					}
+				}
+			}
+		}
+
+		if (startOffset === null) {
+			return null;
+		}
+
+		if (endOffset === null) {
+			endOffset = content.length;
+		}
+
+		return content.substring(startOffset, endOffset).trim();
+	}
+
+	/**
+	 * Extract content for a specific block ID
+	 */
+	extractByBlockId(content: string, cache: CachedMetadata | null, blockId: string): string | null {
+		if (!cache?.sections) {
+			return null;
+		}
+
+		for (const section of cache.sections) {
+			if (section.id === blockId) {
+				return content.substring(
+					section.position.start.offset,
+					section.position.end.offset
+				).trim();
+			}
+		}
+
+		return null;
+	}
+
+	/**
+	 * Resolve a reference to content
+	 */
+	async resolveReference(ref: ContentReference): Promise<string | null> {
+		// Find the file
+		const file = this.app.metadataCache.getFirstLinkpathDest(ref.noteName, '');
+		if (!file) {
+			return null;
+		}
+
+		const content = await this.app.vault.read(file);
+		const cache = this.app.metadataCache.getFileCache(file);
+
+		if (ref.blockId) {
+			return this.extractByBlockId(content, cache, ref.blockId);
+		}
+
+		if (ref.headingPath.length > 0) {
+			return this.extractByHeadingPath(content, cache, ref.headingPath);
+		}
+
+		return content;
+	}
+
+	/**
+	 * Calculate token estimate for a selection
+	 */
+	estimateSelectionTokens(selection: FileSelection): number {
+		const content = this.extractSelectedContent(selection);
+		return estimateTokens(content);
+	}
+
+	/**
+	 * Toggle heading selection (including children)
+	 */
+	toggleHeading(heading: HeadingNode, selected: boolean): void {
+		heading.selected = selected;
+		for (const child of heading.children) {
+			this.toggleHeading(child, selected);
+		}
+	}
+
+	/**
+	 * Update parent selection based on children
+	 */
+	updateParentSelection(headings: HeadingNode[]): void {
+		for (const h of headings) {
+			if (h.children.length > 0) {
+				this.updateParentSelection(h.children);
+				// Parent is selected if any child is selected
+				h.selected = h.children.some(c => c.selected);
+			}
+		}
+	}
+}
+
+// === Heading Flattening for Display ===
+
+export interface FlatHeading {
+	heading: HeadingNode;
+	depth: number;
+	path: string[];
+}
+
+export function flattenHeadings(headings: HeadingNode[], depth = 0, path: string[] = []): FlatHeading[] {
+	const result: FlatHeading[] = [];
+
+	for (const h of headings) {
+		const currentPath = [...path, h.heading];
+		result.push({ heading: h, depth, path: currentPath });
+		result.push(...flattenHeadings(h.children, depth + 1, currentPath));
+	}
+
+	return result;
+}
+
+// === Token Counter ===
+
+export function countSelectionTokens(selections: FileSelection[]): number {
+	let total = 0;
+	const selector = new ContentSelector(null as unknown as App); // We only need extraction logic
+
+	for (const sel of selections) {
+		if (sel.selected) {
+			// This is a simplified count - in real usage we'd use the actual selector
+			const content = sel.fullContent;
+			total += estimateTokens(content);
+		}
+	}
+
+	return total;
+}
diff --git a/src/file-selector-modal.ts b/src/file-selector-modal.ts
new file mode 100644
index 0000000..b0fb7a0
--- /dev/null
+++ b/src/file-selector-modal.ts
@@ -0,0 +1,311 @@
+import { App, Modal, TFile, TFolder } from 'obsidian';
+import ClaudeContextPlugin from './main';
+import {
+	ContentSelector,
+	FileSelection,
+	HeadingNode,
+	flattenHeadings,
+} from './content-selector';
+import { estimateTokens } from './history';
+
+export interface FileSelectionResult {
+	selections: FileSelection[];
+	totalTokens: number;
+}
+
+export class FileSelectorModal extends Modal {
+	plugin: ClaudeContextPlugin;
+	selector: ContentSelector;
+	selections: FileSelection[] = [];
+	onConfirm: (result: FileSelectionResult) => void;
+
+	// UI elements for live update
+	tokenDisplay: HTMLElement | null = null;
+
+	constructor(
+		app: App,
+		plugin: ClaudeContextPlugin,
+		onConfirm: (result: FileSelectionResult) => void
+	) {
+		super(app);
+		this.plugin = plugin;
+		this.selector = new ContentSelector(app);
+		this.onConfirm = onConfirm;
+	}
+
+	async onOpen() {
+		const { contentEl } = this;
+		contentEl.empty();
+		contentEl.addClass('claude-context-file-selector');
+		contentEl.style.minWidth = '500px';
+
+		contentEl.createEl('h2', { text: 'Select Context Content' });
+
+		// Token counter
+		const tokenContainer = contentEl.createDiv({ cls: 'token-counter' });
+		tokenContainer.style.padding = '10px';
+		tokenContainer.style.backgroundColor = 'var(--background-secondary)';
+		tokenContainer.style.borderRadius = '4px';
+		tokenContainer.style.marginBottom = '15px';
+		tokenContainer.style.display = 'flex';
+		tokenContainer.style.justifyContent = 'space-between';
+		tokenContainer.style.alignItems = 'center';
+
+		this.tokenDisplay = tokenContainer.createEl('span', { text: 'Calculating...' });
+
+		const selectAllContainer = tokenContainer.createDiv();
+		const selectAllBtn = selectAllContainer.createEl('button', { text: 'Select All' });
+		selectAllBtn.style.marginRight = '8px';
+		selectAllBtn.addEventListener('click', () => this.selectAll(true));
+
+		const deselectAllBtn = selectAllContainer.createEl('button', { text: 'Deselect All' });
+		deselectAllBtn.addEventListener('click', () => this.selectAll(false));
+
+		// Load files
+		await this.loadFiles();
+
+		// File list
+		const listContainer = contentEl.createDiv({ cls: 'file-list' });
+		listContainer.style.maxHeight = '400px';
+		listContainer.style.overflow = 'auto';
+		listContainer.style.border = '1px solid var(--background-modifier-border)';
+		listContainer.style.borderRadius = '4px';
+
+		this.renderFileList(listContainer);
+		this.updateTokenCount();
+
+		// Buttons
+		const buttonContainer = contentEl.createDiv({ cls: 'button-container' });
+		buttonContainer.style.display = 'flex';
+		buttonContainer.style.justifyContent = 'flex-end';
+		buttonContainer.style.gap = '10px';
+		buttonContainer.style.marginTop = '15px';
+
+		const cancelBtn = buttonContainer.createEl('button', { text: 'Cancel' });
+		cancelBtn.addEventListener('click', () => this.close());
+
+		const confirmBtn = buttonContainer.createEl('button', { text: 'Use Selection', cls: 'mod-cta' });
+		confirmBtn.addEventListener('click', () => {
+			this.onConfirm({
+				selections: this.selections,
+				totalTokens: this.calculateTotalTokens(),
+			});
+			this.close();
+		});
+	}
+
+	private async loadFiles() {
+		const folder = this.app.vault.getAbstractFileByPath(this.plugin.settings.contextFolder);
+
+		if (!folder || !(folder instanceof TFolder)) {
+			return;
+		}
+
+		const excludedFiles = this.plugin.settings.excludedFiles.map(f => f.toLowerCase());
+
+		const files = folder.children
+			.filter((f): f is TFile =>
+				f instanceof TFile &&
+				f.extension === 'md' &&
+				!excludedFiles.includes(f.name.toLowerCase())
+			)
+			.sort((a, b) => {
+				if (a.basename === 'VAULT') return -1;
+				if (b.basename === 'VAULT') return 1;
+				return a.basename.localeCompare(b.basename);
+			});
+
+		for (const file of files) {
+			const selection = await this.selector.buildFileSelection(file);
+			this.selections.push(selection);
+		}
+	}
+
+	private renderFileList(container: HTMLElement) {
+		container.empty();
+
+		for (const selection of this.selections) {
+			this.renderFileRow(container, selection);
+		}
+	}
+
+	private renderFileRow(container: HTMLElement, selection: FileSelection) {
+		const row = container.createDiv({ cls: 'file-row' });
+		row.style.borderBottom = '1px solid var(--background-modifier-border)';
+
+		// File header
+		const header = row.createDiv({ cls: 'file-header' });
+		header.style.display = 'flex';
+		header.style.alignItems = 'center';
+		header.style.padding = '8px 12px';
+		header.style.gap = '8px';
+		header.style.cursor = 'pointer';
+
+		// Expand/collapse icon
+		const expandIcon = header.createEl('span', {
+			text: selection.headings.length > 0 ? (selection.expanded ? '▼' : '▶') : '•'
+		});
+		expandIcon.style.width = '16px';
+		expandIcon.style.fontSize = '10px';
+
+		// File checkbox
+		const checkbox = header.createEl('input', { type: 'checkbox' });
+		checkbox.checked = selection.selected;
+		checkbox.addEventListener('change', (e) => {
+			e.stopPropagation();
+			selection.selected = checkbox.checked;
+			// Toggle all headings
+			for (const h of selection.headings) {
+				this.selector.toggleHeading(h, selection.selected);
+			}
+			this.renderFileList(container.parentElement as HTMLElement);
+			this.updateTokenCount();
+		});
+
+		// File name
+		const name = header.createEl('span', { text: selection.file.name });
+		name.style.flex = '1';
+		name.style.fontWeight = '500';
+
+		// Token estimate for this file
+		const tokens = this.selector.estimateSelectionTokens(selection);
+		const tokenBadge = header.createEl('span', { text: `~${tokens.toLocaleString()} tokens` });
+		tokenBadge.style.fontSize = '11px';
+		tokenBadge.style.color = 'var(--text-muted)';
+
+		// Heading count
+		if (selection.headings.length > 0) {
+			const headingCount = header.createEl('span', {
+				text: `${this.countSelectedHeadings(selection.headings)}/${this.countTotalHeadings(selection.headings)} sections`
+			});
+			headingCount.style.fontSize = '11px';
+			headingCount.style.color = 'var(--text-muted)';
+			headingCount.style.marginLeft = '8px';
+		}
+
+		// Click to expand
+		if (selection.headings.length > 0) {
+			header.addEventListener('click', (e) => {
+				if ((e.target as HTMLElement).tagName !== 'INPUT') {
+					selection.expanded = !selection.expanded;
+					this.renderFileList(container.parentElement as HTMLElement);
+				}
+			});
+		}
+
+		// Headings (if expanded)
+		if (selection.expanded && selection.headings.length > 0) {
+			const headingsContainer = row.createDiv({ cls: 'headings-container' });
+			headingsContainer.style.backgroundColor = 'var(--background-secondary)';
+			headingsContainer.style.paddingLeft = '20px';
+
+			const flatHeadings = flattenHeadings(selection.headings);
+
+			for (const { heading, depth } of flatHeadings) {
+				this.renderHeadingRow(headingsContainer, heading, depth, selection, container.parentElement as HTMLElement);
+			}
+		}
+	}
+
+	private renderHeadingRow(
+		container: HTMLElement,
+		heading: HeadingNode,
+		depth: number,
+		selection: FileSelection,
+		listContainer: HTMLElement
+	) {
+		const row = container.createDiv({ cls: 'heading-row' });
+		row.style.display = 'flex';
+		row.style.alignItems = 'center';
+		row.style.padding = '4px 12px';
+		row.style.paddingLeft = `${12 + depth * 20}px`;
+		row.style.gap = '8px';
+
+		// Checkbox
+		const checkbox = row.createEl('input', { type: 'checkbox' });
+		checkbox.checked = heading.selected;
+		checkbox.addEventListener('change', () => {
+			this.selector.toggleHeading(heading, checkbox.checked);
+			// Update file selection based on headings
+			selection.selected = selection.headings.some(h => this.hasSelectedHeading(h));
+			this.renderFileList(listContainer);
+			this.updateTokenCount();
+		});
+
+		// Heading level indicator
+		const level = row.createEl('span', { text: `H${heading.level}` });
+		level.style.fontSize = '10px';
+		level.style.color = 'var(--text-muted)';
+		level.style.width = '20px';
+
+		// Heading text
+		const text = row.createEl('span', { text: heading.heading });
+		text.style.flex = '1';
+
+		// Content length
+		const length = heading.position.end - heading.position.start;
+		const chars = row.createEl('span', { text: `${length.toLocaleString()} chars` });
+		chars.style.fontSize = '11px';
+		chars.style.color = 'var(--text-muted)';
+	}
+
+	private hasSelectedHeading(heading: HeadingNode): boolean {
+		if (heading.selected) return true;
+		return heading.children.some(c => this.hasSelectedHeading(c));
+	}
+
+	private countSelectedHeadings(headings: HeadingNode[]): number {
+		let count = 0;
+		for (const h of headings) {
+			if (h.selected) count++;
+			count += this.countSelectedHeadings(h.children);
+		}
+		return count;
+	}
+
+	private countTotalHeadings(headings: HeadingNode[]): number {
+		let count = headings.length;
+		for (const h of headings) {
+			count += this.countTotalHeadings(h.children);
+		}
+		return count;
+	}
+
+	private selectAll(selected: boolean) {
+		for (const selection of this.selections) {
+			selection.selected = selected;
+			for (const h of selection.headings) {
+				this.selector.toggleHeading(h, selected);
+			}
+		}
+
+		const container = this.contentEl.querySelector('.file-list') as HTMLElement;
+		if (container) {
+			this.renderFileList(container);
+		}
+		this.updateTokenCount();
+	}
+
+	private calculateTotalTokens(): number {
+		let total = 0;
+		for (const selection of this.selections) {
+			if (selection.selected) {
+				total += this.selector.estimateSelectionTokens(selection);
+			}
+		}
+		return total;
+	}
+
+	private updateTokenCount() {
+		if (this.tokenDisplay) {
+			const tokens = this.calculateTotalTokens();
+			const fileCount = this.selections.filter(s => s.selected).length;
+			this.tokenDisplay.setText(`${fileCount} files selected · ~${tokens.toLocaleString()} tokens`);
+		}
+	}
+
+	onClose() {
+		const { contentEl } = this;
+		contentEl.empty();
+	}
+}
diff --git a/src/generator.ts b/src/generator.ts
index 7cbd883..a579262 100644
--- a/src/generator.ts
+++ b/src/generator.ts
@@ -342,8 +342,13 @@ export class ContextGeneratorModal extends Modal {
 		});
 		templateInfo.style.marginTop = '5px';
 
-		// Copy with context button
-		new Setting(contentEl)
+		// Copy buttons
+		const copyButtonContainer = contentEl.createDiv();
+		copyButtonContainer.style.display = 'flex';
+		copyButtonContainer.style.gap = '10px';
+		copyButtonContainer.style.marginTop = '10px';
+
+		new Setting(copyButtonContainer)
 			.addButton(btn => btn
 				.setButtonText('Copy Context Now')
 				.onClick(async () => {
@@ -362,6 +367,12 @@ export class ContextGeneratorModal extends Modal {
 					// Copy context with selected template
 					await this.plugin.copyContextToClipboard(false, this.temporaryFreetext, this.selectedTemplateId);
 					this.close();
+				}))
+			.addButton(btn => btn
+				.setButtonText('Select Sections...')
+				.onClick(() => {
+					this.close();
+					this.plugin.openFileSelector();
 				}));
 
 		// === GENERATE BUTTON ===
diff --git a/src/main.ts b/src/main.ts
index e6ae27b..172e047 100644
--- a/src/main.ts
+++ b/src/main.ts
@@ -6,6 +6,8 @@ import { SourceRegistry, formatSourceOutput } from './sources';
 import { TemplateEngine } from './templates';
 import { HistoryManager, HistoryMetadata } from './history';
 import { HistoryModal } from './history-modal';
+import { ContentSelector, FileSelection } from './content-selector';
+import { FileSelectorModal, FileSelectionResult } from './file-selector-modal';
 
 export default class ClaudeContextPlugin extends Plugin {
 	settings: ClaudeContextSettings;
@@ -44,9 +46,21 @@ export default class ClaudeContextPlugin extends Plugin {
 			callback: () => this.openHistory()
 		});
 
+		this.addCommand({
+			id: 'copy-context-selective',
+			name: 'Copy context (select sections)',
+			callback: () => this.openFileSelector()
+		});
+
 		this.addSettingTab(new ClaudeContextSettingTab(this.app, this));
 	}
 
+	openFileSelector() {
+		new FileSelectorModal(this.app, this, async (result) => {
+			await this.copyContextWithSelections(result.selections);
+		}).open();
+	}
+
 	async loadSettings() {
 		const loaded = await this.loadData();
 		this.settings = Object.assign({}, DEFAULT_SETTINGS, loaded);
@@ -232,4 +246,132 @@ export default class ClaudeContextPlugin extends Plugin {
 		}
 		new Notice(message);
 	}
+
+	async copyContextWithSelections(
+		selections: FileSelection[],
+		templateId?: string | null
+	) {
+		const selector = new ContentSelector(this.app);
+
+		// Filter to selected files only
+		const selectedFiles = selections.filter(s => s.selected);
+
+		if (selectedFiles.length === 0) {
+			new Notice('No files selected');
+			return;
+		}
+
+		// Resolve additional sources
+		const registry = new SourceRegistry();
+		const enabledSources = this.settings.sources.filter(s => s.enabled);
+		const resolvedSources = await registry.resolveAll(enabledSources);
+
+		// Check for source errors
+		const errors = resolvedSources.filter(r => r.error);
+		if (errors.length > 0) {
+			const errorNames = errors.map(e => e.source.name).join(', ');
+			new Notice(`Some sources failed: ${errorNames}`, 5000);
+		}
+
+		// Separate prefix and suffix sources
+		const prefixSources = resolvedSources.filter(r => r.source.position === 'prefix' && !r.error);
+		const suffixSources = resolvedSources.filter(r => r.source.position === 'suffix' && !r.error);
+
+		// Build output parts
+		const outputParts: string[] = [];
+
+		// Add prefix sources
+		for (const resolved of prefixSources) {
+			const formatted = formatSourceOutput(resolved, this.settings.showSourceLabels);
+			if (formatted) {
+				outputParts.push(formatted);
+			}
+		}
+
+		// Add selected vault content
+		const vaultParts: string[] = [];
+		for (const selection of selectedFiles) {
+			const content = selector.extractSelectedContent(selection);
+			if (content) {
+				if (this.settings.includeFilenames) {
+					// Include heading info if partial selection
+					const isPartial = !this.isFullFileSelected(selection);
+					const suffix = isPartial ? ' (partial)' : '';
+					vaultParts.push(`# === ${selection.file.name}${suffix} ===\n\n${content}`);
+				} else {
+					vaultParts.push(content);
+				}
+			}
+		}
+		outputParts.push(vaultParts.join(`\n\n${this.settings.separator}\n\n`));
+
+		// Add suffix sources
+		for (const resolved of suffixSources) {
+			const formatted = formatSourceOutput(resolved, this.settings.showSourceLabels);
+			if (formatted) {
+				outputParts.push(formatted);
+			}
+		}
+
+		let combined = outputParts.join(`\n\n${this.settings.separator}\n\n`);
+		const sourceCount = prefixSources.length + suffixSources.length;
+		const fileCount = selectedFiles.length;
+		const totalCount = fileCount + sourceCount;
+
+		// Apply template if specified
+		const effectiveTemplateId = templateId !== undefined ? templateId : this.settings.defaultTemplateId;
+		let templateName: string | null = null;
+
+		if (effectiveTemplateId) {
+			const template = this.settings.promptTemplates.find(t => t.id === effectiveTemplateId);
+			if (template) {
+				const engine = new TemplateEngine(this.app);
+				const context = await engine.buildContext(combined);
+				combined = engine.processTemplate(template.content, context);
+				templateName = template.name;
+			}
+		}
+
+		// Prepare history metadata
+		const historyMetadata: Omit<HistoryMetadata, 'charCount' | 'estimatedTokens'> = {
+			templateId: effectiveTemplateId || null,
+			templateName,
+			includedFiles: selectedFiles.map(s => {
+				const isPartial = !this.isFullFileSelected(s);
+				return isPartial ? `${s.file.path} (partial)` : s.file.path;
+			}),
+			includedSources: [
+				...prefixSources.map(r => r.source.name),
+				...suffixSources.map(r => r.source.name),
+			],
+			activeNote: null,
+		};
+
+		// Copy and save
+		const copyAndSave = async () => {
+			await navigator.clipboard.writeText(combined);
+			this.showCopyNotice(fileCount, sourceCount, templateName);
+			await this.historyManager.saveEntry(combined, historyMetadata);
+		};
+
+		if (this.settings.showPreview) {
+			new PreviewModal(this.app, combined, totalCount, copyAndSave).open();
+		} else {
+			await copyAndSave();
+		}
+	}
+
+	private isFullFileSelected(selection: FileSelection): boolean {
+		if (selection.headings.length === 0) return true;
+
+		const checkAll = (headings: import('./content-selector').HeadingNode[]): boolean => {
+			for (const h of headings) {
+				if (!h.selected) return false;
+				if (!checkAll(h.children)) return false;
+			}
+			return true;
+		};
+
+		return checkAll(selection.headings);
+	}
 }