diff --git a/main.ts b/main.ts
index def93e6..7d5adbd 100644
--- a/main.ts
+++ b/main.ts
@@ -6,7 +6,8 @@ enum FolderNoteType {
 }
 
 interface WaypointSettings {
-	waypointFlag: string
+	folderNotesPrefix: string
+	waypointFlag: string,
 	stopScanAtFolderNotes: boolean,
 	showFolderNotes: boolean,
 	showNonMarkdownFiles: boolean,
@@ -17,6 +18,7 @@ interface WaypointSettings {
 }
 
 const DEFAULT_SETTINGS: WaypointSettings = {
+	folderNotesPrefix: "_",
 	waypointFlag: "%% Waypoint %%",
 	stopScanAtFolderNotes: false,
 	showFolderNotes: false,
@@ -57,8 +59,8 @@ export default class Waypoint extends Plugin {
 				const parentFolder = this.getParentFolder(oldPath);
 				if (parentFolder !== null) {
 					this.foldersWithChanges.add(parentFolder);
+					this.scheduleUpdate();
 				}
-				this.scheduleUpdate();
 			}));
 			this.registerEvent(this.app.vault.on("modify", this.detectWaypointFlag));
 		});
@@ -102,10 +104,11 @@ export default class Waypoint extends Plugin {
 
 	isFolderNote(file: TFile): boolean {
 		if (this.settings.folderNoteType === FolderNoteType.InsideFolder) {
-			return file.basename == file.parent.name;
+			return file.basename == this.settings.folderNotesPrefix + file.parent.name;
 		} else if (this.settings.folderNoteType === FolderNoteType.OutsideFolder) {
 			if (file.parent) {
-				return this.app.vault.getAbstractFileByPath(this.getCleanParentPath(file) + file.basename) instanceof TFolder;
+				const folderName = file.basename.substring(this.settings.folderNotesPrefix.length)
+				return this.app.vault.getAbstractFileByPath(this.getCleanParentPath(file) + folderName) instanceof TFolder;
 			}
 			return false;
 		}
@@ -148,7 +151,7 @@ export default class Waypoint extends Plugin {
 		if (this.settings.folderNoteType === FolderNoteType.InsideFolder) {
 			fileTree = await this.getFileTreeRepresentation(file.parent, file.parent, 0, true);
 		} else if (this.settings.folderNoteType === FolderNoteType.OutsideFolder) {
-			const folder = this.app.vault.getAbstractFileByPath(this.getCleanParentPath(file) + file.basename);
+			const folder = this.app.vault.getAbstractFileByPath(this.getCleanParentPath(file) + file.basename.substring(this.settings.folderNotesPrefix.length));
 			if (folder instanceof TFolder) {
 				fileTree = await this.getFileTreeRepresentation(file.parent, folder, 0, true);
 			}
@@ -186,63 +189,57 @@ export default class Waypoint extends Plugin {
 	 */
 	async getFileTreeRepresentation(rootNode: TFolder, node: TAbstractFile, indentLevel: number, topLevel = false): Promise<string>|null {
 		const bullet = "	".repeat(indentLevel) + "-";
+		let text = ""
+
 		if (node instanceof TFile) {
-			console.log(node)
 			// Print the file name
 			if (node.extension == "md") {
-				if (this.settings.useWikiLinks) {
-					return `${bullet} [[${node.basename}]]`;
-				} else {
-					return `${bullet} [${node.basename}](${this.getEncodedUri(rootNode, node)})`;
-				}
+					text = this.settings.useWikiLinks
+						? `${bullet} [[${node.path}|${node.basename}]]`
+						: `${bullet} [${node.basename}](${this.getEncodedUri(rootNode, node)})`;
 			} else if (this.settings.showNonMarkdownFiles) {
-				if (this.settings.useWikiLinks) {
-					return `${bullet} [[${node.name}]]`;
-				} else {
-					return `${bullet} [${node.name}](${this.getEncodedUri(rootNode, node)})`;
-				}
+					text = this.settings.useWikiLinks
+						? `${bullet} [[${node.path}|${node.name}]]`
+						: `${bullet} [${node.name}](${this.getEncodedUri(rootNode, node)})`;
 			}
-			return null;
+			return text;
+			
 		} else if (node instanceof TFolder) {
-			let text = "";
 			if (!topLevel || this.settings.showEnclosingNote) {
 				// Print the folder name
 				text = `${bullet} **${node.name}**`;
-				let folderNote;
-				if (this.settings.folderNoteType === FolderNoteType.InsideFolder) {
-					folderNote = this.app.vault.getAbstractFileByPath(node.path + "/" + node.name + ".md");
-				} else if (this.settings.folderNoteType === FolderNoteType.OutsideFolder) {
-					if (node.parent) {
-						folderNote = this.app.vault.getAbstractFileByPath(node.parent.path + "/" + node.name + ".md");
-					}
-				}
+				let folderNotePath = "/" + this.settings.folderNotesPrefix + node.name + ".md"
+				folderNotePath = this.settings.folderNoteType === FolderNoteType.InsideFolder
+					? node.path + folderNotePath
+					: this.settings.folderNoteType === FolderNoteType.OutsideFolder && node.parent
+						? node.parent.path + folderNotePath
+						: folderNotePath;
+				const folderNote = this.app.vault.getAbstractFileByPath(folderNotePath);
 				if (folderNote instanceof TFile) {
-					if (this.settings.useWikiLinks) {
-						text = `${bullet} **[[${folderNote.basename}]]**`;
-					} else {
-						text = `${bullet} **[${folderNote.basename}](${this.getEncodedUri(rootNode, folderNote)})**`;
-					}
+						text = this.settings.useWikiLinks
+							? `${bullet} **[[${folderNotePath}|${folderNote.parent.name}]]**`
+							: `${bullet} **[${folderNote.basename}](${this.getEncodedUri(rootNode, folderNote)})**`;
 					if (!topLevel) {
 						if (this.settings.stopScanAtFolderNotes) {
 							return text;
 						} else {
 							const content = await this.app.vault.cachedRead(folderNote);
 							if (content.includes(Waypoint.BEGIN_WAYPOINT) || content.includes(this.settings.waypointFlag)) {
-								return text;
+								// return text;
 							}
 						}
 					}
 				}
 			}
-			if (node.children && node.children.length > 0) {
+			let children = node.children;
+			if (children && children.length > 0) {
 				// Print the files and nested folders within the folder
-				let children = node.children;
 				children = children.sort((a, b) => {
 					return a.name.localeCompare(b.name, undefined, {numeric: true, sensitivity: 'base'});
 				});
 				if (!this.settings.showFolderNotes) {
 					if (this.settings.folderNoteType === FolderNoteType.InsideFolder) {
-						children = children.filter(child => this.settings.showFolderNotes || child.name !== node.name + ".md");
+						children = children.filter(child => this.settings.showFolderNotes || child.name !== this.settings.folderNotesPrefix + node.name + ".md");
 					} else if (this.settings.folderNoteType === FolderNoteType.OutsideFolder) {
 						const folderNames = new Set();
 						for (const element of children) {
@@ -326,10 +323,10 @@ export default class Waypoint extends Plugin {
 		while (folder) {
 			let folderNote;
 			if (this.settings.folderNoteType === FolderNoteType.InsideFolder) {
-				folderNote = this.app.vault.getAbstractFileByPath(folder.path + "/" + folder.name + ".md");
+				folderNote = this.app.vault.getAbstractFileByPath(folder.path + "/" + this.settings.folderNotesPrefix + folder.name + ".md");
 			} else if (this.settings.folderNoteType === FolderNoteType.OutsideFolder) {
 				if (folder.parent) {
-					folderNote = this.app.vault.getAbstractFileByPath(this.getCleanParentPath(folder) + folder.name + ".md");
+					folderNote = this.app.vault.getAbstractFileByPath(this.getCleanParentPath(folder) + this.settings.folderNotesPrefix + folder.name + ".md");
 				}
 			}
 			if (folderNote instanceof TFile) {
@@ -387,6 +384,16 @@ class WaypointSettingsTab extends PluginSettingTab {
 		const {containerEl} = this;
 		containerEl.empty();
 		containerEl.createEl('h2', {text: 'Waypoint Settings'});
+		new Setting(containerEl)
+			.setName("Folder Notes Prefix")
+			.setDesc("Allow prefix to be added to the folder notes filename.")
+			.addText(text => text
+				.setValue(this.plugin.settings.folderNotesPrefix)
+				.onChange(async (value) => {
+					this.plugin.settings.folderNotesPrefix = value;
+					await this.plugin.saveSettings();
+				})
+			);
 		new Setting(this.containerEl)
 			.setName("Folder Note Style")
 			.setDesc("Select the style of folder note used.")
@@ -475,4 +482,4 @@ class WaypointSettingsTab extends PluginSettingTab {
 		descriptionElement.createEl("a", { attr: { "href": "https://twitter.com/IdreesInc" }, text: "@IdreesInc" });
 		postscriptElement.appendChild(descriptionElement);
 	}
-}
+}
\ No newline at end of file
diff --git a/package-lock.json b/package-lock.json
index 9a588c8..e4004f9 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,12 +1,12 @@
 {
 	"name": "waypoint",
-	"version": "1.3.0",
+	"version": "1.4.0",
 	"lockfileVersion": 2,
 	"requires": true,
 	"packages": {
 		"": {
 			"name": "waypoint",
-			"version": "1.3.0",
+			"version": "1.4.0",
 			"license": "MIT",
 			"devDependencies": {
 				"@types/codemirror": "^5.60.5",