cordova config.xml whats valid and whats not? trying to get navigator.notification.alert() to work, failing - iphone

Question

I have been trying to sort this out for a while, and I have been trying to piece one together via google searches.. But I am recently noticing that most of the docs I come or have come across are for older versions of cordova/phonegap. I am using I 3.x or whatever the latest one is. Either way, my config.xml I feel is a mess. Another thing I noticed is I seem to have two config.xml's one is in the www folder, one is right at the same level as the www folder, the copy below is the one at the same level as the www folder which seems to be the one that listens to changes but Im not sure if there is a conflict there either.
I also found a copy of phonegap.js from the examples.. which I think is based on 1.7.0 and not my current version of phonegap/cordova. All in all I am trying to figure this all out so I can use things like the camera, so I can change things like the title of a alert box to go from a long path and file name then my message.
<?xml version='1.0' encoding='utf-8'?>
<widget id="com.domain.coffee" version="2.0.0" xmlns="http://www.w3.org/ns/widgets">
<name>title of app (wont put here)</name>
<description>
my long lengthy description
</description>
<author email="team#domain.com" href="http://www.domain.com">
domain development team
</author>
<content src="index.html" />
<feature name="LocalStorage">
<param name="ios-package" value="CDVLocalStorage" />
</feature>
<feature name="Notification">
<param name="ios-package" value="CDVNotification" />
</feature>
<access origin="*" />
<preference name="KeyboardDisplayRequiresUserAction" value="true" />
<preference name="SuppressesIncrementalRendering" value="false" />
<preference name="UIWebViewBounce" value="true" />
<preference name="TopActivityIndicator" value="gray" />
<preference name="EnableLocation" value="true" />
<preference name="EnableViewportScale" value="false" />
<preference name="AutoHideSplashScreen" value="true" />
<preference name="ShowSplashScreenSpinner" value="true" />
<preference name="MediaPlaybackRequiresUserAction" value="false" />
<preference name="AllowInlineMediaPlayback" value="false" />
<preference name="OpenAllWhitelistURLsInWebView" value="false" />
<preference name="BackupWebStorage" value="cloud" />
<preference name="fullscreen" value="true" />
<preference name="webviewbounce" value="true" />
<plugins>
<plugin name="Device" value="CDVDevice" />
<plugin name="Logger" value="CDVLogger" />
<plugin name="Compass" value="CDVLocation" />
<plugin name="Accelerometer" value="CDVAccelerometer" />
<plugin name="Camera" value="CDVCamera" />
<plugin name="NetworkStatus" value="CDVConnection" />
<plugin name="Contacts" value="CDVContacts" />
<plugin name="Debug Console" value="CDVDebugConsole" />
<plugin name="Echo" value="CDVEcho" />
<plugin name="File" value="CDVFile" />
<plugin name="FileTransfer" value="CDVFileTransfer" />
<plugin name="Geolocation" value="CDVLocation" />
<plugin name="Media" value="CDVSound" />
<plugin name="Capture" value="CDVCapture" />
<plugin name="SplashScreen" value="CDVSplashScreen" />
<plugin name="Battery" value="CDVBattery" />
<plugin name="Globalization" value="CDVGlobalization" />
<plugin name="InAppBrowser" value="CDVInAppBrowser" />
<plugin name="org.apache.cordova.facebook.Connect" value="FacebookConnectPlugin" />
</plugins>
</widget>
note I have followed this most recently:
http://docs.phonegap.com/en/3.0.0/cordova_notification_notification.md.html#notification.alert
also an example of my message attempts would be:
navigator.notification.alert("my fancy message", "my title", "OK");