I am having an issue with DOMDocument and whitespace. Currently I have two types of XML files. One file was created manually about a year ago, I will call this file A. The second file, file B, is being generated using a PHP DOMDocument. I have been trying very hard (unsuccessfully) to make the whitespace in file A match file B.
Here's how it works... The user is given an option to add new <Slide> elements to the XML file. After new slides have been added the user has the option to add new <Items> to the XML file as a child of the <Slide> element.
When I add a <Slide> element to file B it works like a charm. I can even add a new <Item> element with zero problem. However, when I try to access the new <Identifier> element I just added in file B using the second PHP script below with $order != 'remove' I miss the node by one and select <Information/> instead. 
It appears that manually created file A has white space that is not present in my generated file B. I have experimented with the preserveWhitespace property but it did not help.
Are there any suggestions on how I can correct this problem. Constructive criticism is also welcome as this is my first shot at dynamic XML manipulation. I apologize for the length and appreciate your time!!
File A - Created Manually - I am trying to match this file!
<?xml version="1.0" encoding="UTF-8"?>
<root>
<Areas>Head & Neck</Areas>
<Area>Head & Neck</Area>
<Type>Angiograph</Type>
<Slide>Ag-01a
    <Title>Catheter Angiography</Title>
    <Item1>
        <Identifier interestCoord=".51,.73" locator="point" labelBool="true" labelTxt="" leaderBool="true">Aortic Arch
        </Identifier>
        <Information/>
        <Question A="" B="" C="" D="" E="" Answer=""/>
    </Item1>
             .... More Items 
File B - Before user adds <Slide>. This portion is created Manually. A template if you will. After the user enters slide names new slides are generated using the chunk of code below. 
<?xml version="1.0" encoding="UTF-8"?>
<root>
<Areas>Head & Neck</Areas>
<Area>Head & Neck</Area>
<Type>Brain Sections</Type>
</root>
File B - After users adds new <Slide> and <Item>. Formatting shown represents formatting created by DOMDocument. I think this is where the error is occuring! Whitespace!!!
<Slide>Ag-09a
    <Title>Catheter Angiography</Title>
<Item1><Identifier locator="point" interestCoord="0.143,0.65" labelBool="true" labelTxt="" leaderBool="false">Orbit</Identifier><Information/><Question A="" B="" C="" D="" E="" Answer=""/></Item1></Slide>
PHP script used to add new <Slide> elements to XML
<?php
session_start();
//Constants
$SECTION_SEP = "========================================================================</br>";
//Variables used to construct file path
$area = trim($_POST['area']);
$slideType = trim($_POST['slideType']);
$rawSlides = trim($_POST['theseSlides']);
$newSlideList = explode(",", $rawSlides);
$fileLocation = "../XML/".$area."/".$slideType."/".$area.".XML";
$dom = new DOMDocument();
echo('New DOMDocument created!</br>');
$dom->load($fileLocation);
echo('XML file loaded!</br>');
/*$dom->preserveWhiteSpace = false;
echo('White space removed!</br>');*/
$dom->documentElement;
echo('DOM initialized!</br>');
if ($dom->getElementsByTagName('Slide')->length == 0){  //New file with no slides
foreach ($newSlideList as $slide){
    $newSlide = $dom->createElement('Slide', $slide);
    $newTitle = $dom->createElement('Title', 'Scan');
    //Add the title element to the Item
    $newSlide->appendChild($newTitle);
    $dom->childNodes->item(0)->appendChild($newSlide);
    echo($slide." has been added to the list!</br>");
 }
} else {
$locators = $dom->getElementsByTagName('Slide');
}
if($dom->save($fileLocation)){
echo("File saved successfully!!");
}else echo("There was a problem saving the file!");
PHP script used to add/edit/remove <Item> and <Identifier> nodes depending on value of $orders == WARNING! Lengthy :/
<?php
session_start();
//Constants
$SECTION_SEP = "========================================================================</br>";
//Variables used to construct file path
$area = trim($_POST['area']);
$slideType = trim($_POST['slideType']);
$fileLocation = "../XML/".$area."/".$slideType."/".$area.".XML";
//echo("File location:".$fileLocation);
//Current data (c_ for current)
$c_poi = "";
$c_type = "";
$c_lblBool = "";
$c_lblOverride = "";
$c_leaderBool = "";
//Determine if this visit is for new or old data
$orders = trim($_POST['orders']);
//Variables used to replace information in XML file loaded below (n_ for new)
$n_slideName = trim($_POST['slideName']); //slide name in view format ie Ag-01a
$n_identName = trim($_POST['ident']); //contains multiple information separated by comma ie 0,Aortic Arch
$n_type = trim($_POST['type']); //locator type
$n_poi = trim($_POST['poi']);
$n_lblBool = trim($_POST['lblBool']);
$n_lblOverride = trim($_POST['lblOverride']);
echo("Modified: ".date('c')."</br>");
$dom = new DOMDocument();
echo('New DOMDocument created!</br>');
$dom->load($fileLocation);
echo('XML file loaded!</br>');
/*$dom->preserveWhiteSpace = false;
echo('White space removed!</br>');*/
$dom->documentElement;
echo('DOM initialized!</br>');
$locators = $dom->getElementsByTagName('Slide');
echo($locators->length.' elements retrieved</br>');
$slideEntryFound = false;
$identEntryFound = false;
$identAttributesFound = false;
echo($SECTION_SEP);
//Locate the correct slide node
foreach ($locators as $locator){
//If there is a match, store the infomation
// rawSlide[x].childNode[0].nodeValue
if(strcmp(trim($locator->childNodes->item(0)->nodeValue),$n_slideName) == 0){
    $slideEntryFound = true;
    $slideChildren = $locator->childNodes;
    //Locate the correct identifier node
    foreach($slideChildren as $child){
        if( strcmp(trim($child->nodeValue), substr($n_identName,strpos($n_identName,",")+1)) == 0){
            $identEntryFound = true;
            if (strcmp($orders, "remove") == 0){//Removing an element
                echo("The identifier being removed is: ".trim($child->nodeValue."</br>"));
                echo("The node path is: ".($child->childNodes->item(1)->getNodePath())."</br>");
                echo($SECTION_SEP);
                $locator->removeChild($child);
                echo("Identifier successfully removed!</br>");
                echo($SECTION_SEP);
                break;
            } else {//Not removing anything - Adding or Editing
                echo("The identifier being modified is: ".trim($child->nodeValue."</br>"));
                echo("The node path is: ".($child->childNodes->item(1)->getNodePath())."</br>");
                echo($SECTION_SEP);
                if($child->childNodes->item(1)->hasAttributes()){
                    $identAttributesFound = true;
                    $c_poi = $child->childNodes->item(1)->getAttribute('interestCoord');
                     echo("--Current interestCoord: ".$c_poi."</br>");
                     echo("++New interestCoord: ".$n_poi."</br>");
                    if(strcmp($c_poi, $n_poi) != 0){
                       $child->childNodes->item(1)->setAttribute('interestCoord',$n_poi);
                    }
                    $c_type = $child->childNodes->item(1)->getAttribute('locator');
                     echo("--Current locator: ".$c_type."</br>");
                     echo("++New locator: ".$n_type."</br>");
                    $c_lblBool = $child->childNodes->item(1)->getAttribute('labelBool');
                     echo("--Current labelBool: ".$c_lblBool."</br>");
                     //echo("++New labelBool: ".$n_lblBool."</br>");
                    $c_lblOverride = $child->childNodes->item(1)->getAttribute('labelTxt');
                     echo("--Current labelOverride: ".$c_lblOverride."</br>");
                     echo("++New labelOverride: ".$n_lblOverride."</br>");
                    $c_leaderBool = $child->childNodes->item(1)->getAttribute('leaderBool');
                     echo("--Current leaderBool: ".$c_leaderBool."</br>");
                     //echo("++New leaderBool: ".$n_leaderBool."</br>");
                    if($n_lblOverride != ""){
                        echo("**A new label override was detected. The identifier will have the alias ".$n_lblOverride.".");
                    }
               break;
            } else echo("Fatal Error - Node does not contain attributes!</br>");
            if($identEntryFound == true && $identAttributesFound == false)
                echo("Error - Attribute entry not found!");
            break;
            }
        }
    }
    if($slideEntryFound == true && $identEntryFound == false && $orders != "remove"){
        echo("The identifier was not found... creating a new identifier!</br>");
     //Create a new Element
        $newElement = $dom->createElement("Item".((integer)(substr($n_identName,0,strpos($n_identName,",")))+1));
        echo("New element created!!</br>");
        //Create new Item children
        $newSubElem = $dom->createElement("Identifier", substr($n_identName,strpos($n_identName,",")+1));
        $newSubElem->setAttribute('locator',$n_type);
        $newSubElem ->setAttribute('interestCoord',$n_poi);
        $newSubElem->setAttribute('labelBool', $n_lblBool);
        $newSubElem->setAttribute('labelTxt', $n_lblOverride);
        //TODO link this next one to a variable instead of hard coding
        $newSubElem->setAttribute('leaderBool', "false");
        //Info Child
        $newInfoElem = $dom->createElement("Information");
        //Question Child
        $newQuestion = $dom->createElement("Question");
            $newQuestion->setAttribute('A', "");
            $newQuestion->setAttribute('B', "");
            $newQuestion->setAttribute('C', "");
            $newQuestion->setAttribute('D', "");
            $newQuestion->setAttribute('E', "");
            $newQuestion->setAttribute('Answer', "");
        //Add new children to main Item
        $newElement->appendChild($newSubElem);
        $newElement->appendChild($newInfoElem);
        $newElement->appendChild($newQuestion);
        $locator->appendChild($newElement);
        echo("New identifier added!!</br>");
    break;
    }
} else {
}
}
if($slideEntryFound == false)
echo("Error - Slide entry not found!");
if($dom->save($fileLocation)){
echo("File saved successfully!!");
echo('<div id="phpHandleBtns>"></br><form><button type="submit" id="continueEdit" formaction="../edit.php">Continue Editing</button>'.
    '</br><button type="submit" id="doneEdit" formaction="../main.php">Done Editing</button></form></div>');
}else echo("There was a problem saving the file!");
?>