diff --git a/main.ts b/main.ts
index 27d6c85..2933223 100644
--- a/main.ts
+++ b/main.ts
@@ -1,10 +1,12 @@
-import { App, debounce, Plugin, PluginSettingTab, Setting, TAbstractFile, TFile, TFolder } from 'obsidian';
+import {App, debounce, Plugin, PluginSettingTab, Setting, TAbstractFile, TFile, TFolder, Vault} from 'obsidian';
 
 interface WaypointSettings {
 	waypointFlag: string
 	stopScanAtFolderNotes: boolean,
 	showFolderNotes: boolean,
 	debugLogging: boolean,
+	ignoredFolders: string[],
+	root: string
 	useWikiLinks: boolean
 }
 
@@ -13,7 +15,9 @@ const DEFAULT_SETTINGS: WaypointSettings = {
 	stopScanAtFolderNotes: false,
 	showFolderNotes: false,
 	debugLogging: false,
-	useWikiLinks: true
+	useWikiLinks: true,
+	ignoredFolders: ["Templates"],
+	root: null
 }
 
 export default class Waypoint extends Plugin {
@@ -29,7 +33,8 @@ export default class Waypoint extends Plugin {
 			// Register events after layout is built to avoid initial wave of 'create' events
 			this.registerEvent(this.app.vault.on("create", (file) => {
 				this.log("create " + file.name);
-				this.foldersWithChanges.add(file.parent);
+				const folderParent = this.getParentFolder(file.path);
+				this.foldersWithChanges.add(folderParent);
 				this.scheduleUpdate();
 			}));
 			this.registerEvent(this.app.vault.on("delete", (file) => {
@@ -42,7 +47,8 @@ export default class Waypoint extends Plugin {
 			}));
 			this.registerEvent(this.app.vault.on("rename", (file, oldPath) => {
 				this.log("rename " + file.name);
-				this.foldersWithChanges.add(file.parent);
+				const parentFolderOrigin = this.getParentFolder(file.path);
+				this.foldersWithChanges.add(parentFolderOrigin);
 				const parentFolder = this.getParentFolder(oldPath);
 				if (parentFolder !== null) {
 					this.foldersWithChanges.add(parentFolder);
@@ -54,6 +60,17 @@ export default class Waypoint extends Plugin {
 
 		// This adds a settings tab so the user can configure various aspects of the plugin
 		this.addSettingTab(new WaypointSettingsTab(this.app, this));
+
+		// Add in a hotkey to update the waypoint
+		this.addCommand({
+			id: "update-waypoint",
+			name: "Update waypoint in current file",
+			hotkeys: [{
+				modifiers: ["Ctrl"],
+				key: "w"
+			}],
+			callback: () => { this.updateWaypoint(this.app.workspace.getActiveFile()) }
+		})
 	}
 
 	onunload() {
@@ -74,10 +91,16 @@ export default class Waypoint extends Plugin {
 					this.log("Found waypoint flag in folder note!");
 					await this.updateWaypoint(file);
 					await this.updateParentWaypoint(file.parent, false);
-					return;	
+					return;
+				} else if (this.outsideFolderPath(file)) {
+					await this.updateWaypoint(file);
+					await this.updateParentWaypoint(this.outsideFolderPath(file), false);
+					return;
 				} else if (file.parent.isRoot()) {
 					this.log("Found waypoint flag in root folder.");
-					this.printWaypointError(file, `%% Error: Cannot create a waypoint in the root folder of your vault. For more information, check the instructions [here](https://github.com/IdreesInc/Waypoint) %%`);
+					this.settings.root = file.name;
+					await this.saveSettings();
+					await this.updateWaypoint(file);
 					return;
 				} else {
 					this.log("Found waypoint flag in invalid note.");
@@ -89,6 +112,14 @@ export default class Waypoint extends Plugin {
 		this.log("No waypoint flags found.");
 	}
 
+	outsideFolderPath(file:TFile) {
+		const folderNotePath = this.app.vault.getAbstractFileByPath(file.path.replace('.md', ''));
+		if (folderNotePath && folderNotePath instanceof TFolder) {
+			return folderNotePath;
+		}
+		return null;
+	}
+
 	async printWaypointError(file: TFile, error: string) {
 		this.log("Creating waypoint error in " + file.path);
 		const text = await this.app.vault.read(file);
@@ -114,7 +145,12 @@ export default class Waypoint extends Plugin {
 	 */
 	async updateWaypoint(file: TFile) {
 		this.log("Updating waypoint in " + file.path);
-		const fileTree = await this.getFileTreeRepresentation(file.parent, 0, true);
+		const parentFolder = this.getParentFolder(file.path);
+		let fileTree = await this.getFileTreeRepresentation(parentFolder, 0, true);
+		if (parentFolder.isRoot()) {
+			const splitFileTree = fileTree.split("\n");
+			fileTree = `- **[[${file.basename}]]**\n${splitFileTree.slice(1).join("\n")}`
+		}
 		const waypoint = `${Waypoint.BEGIN_WAYPOINT}\n${fileTree}\n\n${Waypoint.END_WAYPOINT}`;
 		const text = await this.app.vault.read(file);
 		const lines: string[] = text.split("\n");
@@ -148,7 +184,8 @@ export default class Waypoint extends Plugin {
 	async getFileTreeRepresentation(node: TAbstractFile, indentLevel: number, topLevel = false): Promise<string>|null {
 		const bullet = "	".repeat(indentLevel) + "-";
 		if (node instanceof TFile) {
-			if (node.path.endsWith(".md")) {
+			// Check for the parent being the root because otherwise the "root note" would be included in the tree
+			if (node.path.endsWith(".md") && !node.parent.isRoot()) {
 				if (this.settings.useWikiLinks) {
 					return `${bullet} [[${node.basename}]]`;
 				} else {
@@ -157,6 +194,7 @@ export default class Waypoint extends Plugin {
 			}
 			return null;
 		} else if (node instanceof TFolder) {
+			if (this.settings.ignoredFolders.includes(node.path)) { return null }
 			let text = `${bullet} **${node.name}**`;
 			const folderNote = this.app.vault.getAbstractFileByPath(node.path + "/" + node.name + ".md");
 			if (folderNote instanceof TFile) {
@@ -183,8 +221,8 @@ export default class Waypoint extends Plugin {
 				}).filter(child => this.settings.showFolderNotes || child.name !== node.name + ".md");
 				if (children.length > 0) {
 					text += "\n" + (await Promise.all(children.map(child => this.getFileTreeRepresentation(child, indentLevel + 1))))
-					.filter(Boolean)
-					.join("\n");
+						.filter(Boolean)
+						.join("\n");
 				}
 				return text;
 			} else {
@@ -237,17 +275,29 @@ export default class Waypoint extends Plugin {
 	async locateParentWaypoint(node: TAbstractFile, includeCurrentNode: boolean): Promise<TFile> {
 		this.log("Locating parent waypoint of " + node.name);
 		let folder = includeCurrentNode ? node : node.parent;
-		while (folder) {
-			const folderNote = this.app.vault.getAbstractFileByPath(folder.path + "/" + folder.name + ".md");
-			if (folderNote instanceof TFile) {
-				this.log("Found folder note: " + folderNote.path);
-				const text = await this.app.vault.cachedRead(folderNote);
+		if (node.parent.isRoot() && this.settings.root !== null) {
+			const file = this.app.vault.getAbstractFileByPath(this.settings.root)
+			if (file instanceof TFile) {
+				this.log("Found folder note: " + file.path);
+				const text = await this.app.vault.cachedRead(file);
 				if (text.includes(Waypoint.BEGIN_WAYPOINT) || text.includes(this.settings.waypointFlag)) {
 					this.log("Found parent waypoint!");
-					return folderNote;
+					return file;
 				}
 			}
-			folder = folder.parent;
+		} else {
+			while (folder) {
+				const folderNote = this.app.vault.getAbstractFileByPath(folder.path + "/" + folder.name + ".md");
+				if (folderNote instanceof TFile) {
+					this.log("Found folder note: " + folderNote.path);
+					const text = await this.app.vault.cachedRead(folderNote);
+					if (text.includes(Waypoint.BEGIN_WAYPOINT) || text.includes(this.settings.waypointFlag)) {
+						this.log("Found parent waypoint!");
+						return folderNote;
+					}
+				}
+				folder = folder.parent;
+			}
 		}
 		this.log("No parent waypoint found.");
 		return null;
@@ -260,8 +310,11 @@ export default class Waypoint extends Plugin {
 	 */
 	getParentFolder(path: string): TFolder {
 		const abstractFile = this.app.vault.getAbstractFileByPath(path.split("/").slice(0, -1).join("/"));
+		const abstractOutsideFolder = this.app.vault.getAbstractFileByPath(path.replace('.md', ''));
 		if (abstractFile instanceof TFolder) {
 			return abstractFile;
+		} else if (abstractOutsideFolder instanceof TFolder) {
+			return abstractOutsideFolder;
 		} else {
 			return null;
 		}
@@ -269,7 +322,7 @@ export default class Waypoint extends Plugin {
 
 	log(message: string) {
 		if (this.settings.debugLogging) {
-			console.log(message);			
+			console.log(message);
 		}
 	}
 
@@ -340,6 +393,28 @@ class WaypointSettingsTab extends PluginSettingTab {
 					await this.plugin.saveSettings();
 				})
 			);
+		new Setting(containerEl)
+			.setName("Ignored folders")
+			.setDesc("Folders that Waypoint should ignore")
+			.addText(text => text
+				.setPlaceholder(DEFAULT_SETTINGS.ignoredFolders.join(","))
+				.setValue(this.plugin.settings.ignoredFolders.join(", "))
+				.onChange(async (value) => {
+					const previous = this.plugin.settings.ignoredFolders;
+					this.plugin.settings.ignoredFolders = value.split(/\s*,\s*/);
+					await this.plugin.saveSettings();
+
+					// Get a list of all new and old folders that need updating
+					const allFolders = [...new Set([...previous, ...this.plugin.settings.ignoredFolders])]
+					for (let i = 0; i < allFolders.length; i++) {
+						const file = this.app.vault.getAbstractFileByPath(allFolders[i]);
+						if (file === null) { continue }
+						await this.plugin.locateParentWaypoint(file, false).then((file) => {
+							if (file !== null) { this.plugin.updateWaypoint(file) }
+						})
+					}
+				})
+			);
 		const postscriptElement = containerEl.createEl("div", {
 			cls: "setting-item",
 		});
diff --git a/package-lock.json b/package-lock.json
index 88445a8..ef1964d 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,12 +1,20 @@
 {
 	"name": "waypoint",
+<<<<<<< HEAD
+	"version": "1.2.0",
+=======
 	"version": "1.1.0",
+>>>>>>> FolderRoot/Master
 	"lockfileVersion": 2,
 	"requires": true,
 	"packages": {
 		"": {
 			"name": "waypoint",
+<<<<<<< HEAD
+			"version": "1.2.0",
+=======
 			"version": "1.1.0",
+>>>>>>> FolderRoot/Master
 			"license": "MIT",
 			"devDependencies": {
 				"@types/codemirror": "^5.60.5",