Added Scholar.Prefs, a front-end to the preferences service with simple get(pref) and set(pref, value) methods that will retrieve and set based on the type of the default value, which I believe should generally should fine -- for more fine-grained control, use Scholar.Prefs.prefBranch to access the branch directly

Scholar.Prefs also registers itself as a preferences observer and can be used to trigger actions when certain prefs are changed by editing the switch statement in the observe() method

Updated preferences.js to use Scholar.Prefs

chrome/chromeFiles/content/scholar/preferences.js

@@ -1,5 +1,3 @@
-var prefManager = Components.classes["@mozilla.org/preferences-service;1"]
-                                .getService(Components.interfaces.nsIPrefBranch);
 var autoUpdateBox;
 
 /*
@@ -10,16 +8,19 @@ var autoUpdateBox;
 			b) add lines to init() function
 			c) add line to accept() function
 		3) add a control to prefs.xul
+		4) (Optional) To add an observer for a preference change,
+			add an appropriate case in the switch statement
+			in Scholar.Prefs.observe()
 */
 
 function init()
 {	
 	autoUpdateBox = document.getElementById('autoUpdateBox');
-	autoUpdateBox.checked = prefManager.getBoolPref('extensions.scholar.automaticScraperUpdates');
+	autoUpdateBox.checked = Scholar.Prefs.get('automaticScraperUpdates');
 
 }
 
 function accept()
 {
-	prefManager.setBoolPref('extensions.scholar.automaticScraperUpdates', autoUpdateBox.checked);
+	Scholar.Prefs.set('automaticScraperUpdates', autoUpdateBox.checked)
 }

chrome/chromeFiles/content/scholar/xpcom/scholar.js

@@ -39,6 +39,9 @@ var Scholar = new function(){
 			return false;
 		}
 		
+		// Load in the preferences branch for the extension
+		Scholar.Prefs.init();
+		
 		// Load in the extension version from the extension manager
 		var nsIUpdateItem = Components.interfaces.nsIUpdateItem;
 		var gExtensionManager =
@@ -281,6 +284,99 @@ var Scholar = new function(){
 
 
 
+Scholar.Prefs = new function(){
+	// Privileged methods
+	this.init = init;
+	this.get = get;
+	this.set = set;
+	
+	this.register = register;
+	this.unregister = unregister;
+	this.observe = observe;
+	
+	// Public properties
+	this.prefBranch; // set in Scholar.init()
+	
+	function init(){
+		var prefs = Components.classes["@mozilla.org/preferences-service;1"]
+						.getService(Components.interfaces.nsIPrefService);
+		this.prefBranch = prefs.getBranch("extensions.scholar.");
+		
+		// Register observer to handle pref changes
+		this.register();
+	}
+	
+	
+	/**
+	* Retrieve a preference
+	**/
+	function get(pref){
+		try {
+			switch (this.prefBranch.getPrefType(pref)){
+				case this.prefBranch.PREF_BOOL:
+					return this.prefBranch.getBoolPref(pref);
+				case this.prefBranch.PREF_STRING:
+					return this.prefBranch.getCharPref(pref);
+				case this.prefBranch.PREF_INT:
+					return this.prefBranch.getIntPref(pref);
+			}
+		}
+		catch (e){
+			throw ("Invalid preference '" + pref + "'");
+		}
+	}
+	
+	
+	/**
+	* Set a preference
+	**/
+	function set(pref, value){
+		try {
+			switch (this.prefBranch.getPrefType(pref)){
+				case this.prefBranch.PREF_BOOL:
+					return this.prefBranch.setBoolPref(pref, value);
+				case this.prefBranch.PREF_STRING:
+					return this.prefBranch.setCharPref(pref, value);
+				case this.prefBranch.PREF_INT:
+					return this.prefBranch.setIntPref(pref, value);
+			}
+		}
+		catch (e){
+			throw ("Invalid preference '" + pref + "'");
+		}
+	}
+	
+	
+	//
+	// Methods to register a preferences observer
+	//
+	function register(){
+		this.prefBranch.QueryInterface(Components.interfaces.nsIPrefBranch2);
+		this.prefBranch.addObserver("", this, false);
+	}
+	
+	function unregister(){
+		if (!this.prefBranch){
+			return;
+		}
+		this.prefBranch.removeObserver("", this);
+	}
+	
+	function observe(subject, topic, data){
+		if(topic!="nsPref:changed"){
+			return;
+		}
+		// subject is the nsIPrefBranch we're observing (after appropriate QI)
+		// data is the name of the pref that's been changed (relative to subject)
+		switch (data){
+			case "pref1":
+				// pref1 changed
+				break;
+		}
+	}
+}
+
+
 
 /**
 * Class for creating hash arrays that behave a bit more sanely