Complete docs index page. Updated SaveSetup to use function calls rather than...

Complete docs index page. Updated SaveSetup to use function calls rather than using the interface to submit the setup configuration. Working on GlobalJS page to document the WhatPage.js file. Testing code portion of docs as well.

WAMI/WAMI/SaveSetup.js

 (function() {
     var overdue = document.getElementById("IgnoreOverdueFines");
-    var okBtn = document.getElementById("OkBtn");
 
     overdue.checked = true;
-    okBtn.click();
+    OnOk(returnObjById("CollectionList2"), collectionsArray, CheckShelfOrder, IgnoreOverdueFines);
 })();
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docs/GlobalJS.md

 # Global Scope JavaScript
-The JS function specified below is run on every page.
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+The JS function specified below is run on every page.
+
+#### [WhatPage.js](../WAMI/WAMI/WhatPage.js)
+Will determine what page, and therefore the step in the inventory process currently at. This is accomplished by obtaining the URL from the page and search for certain strings in the URL to determine what page the script executes on. 
+
+```javascript
+var url = document.URL;
+
+if (url.search("Login") != -1)
+    return 0;
+else if (url.search("Setup") != -1)
+    return 1;
+else if (url.search("Scan") != -1)
+    return 2;
+else if (url.search("Action") != -1)
+    return 3;
+else
+    return -1;
+```
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docs/index.md

 # JavaScript Index
 This index provides an overview of the different JavaScript functions included in the application. These functions are separated into  that are included in this application, which are listed below broken down based upon scope of operation (i.e. page file is utilized on). 
 
-## [Global](/GlobalJs.md/)
+## [Global](GlobalJs.md)
 ##### WhatPage.js
 File contains function to determine current page, or location in scan process, of the current inventory session.
 
-## [Login Page](/LoginJS.md/)
+## [Login Page](LoginJS.md)
 #### Login.js
+Contains function to input login username and password, retrieve and select the correct location information, as well as submit this information and login to RTI.
 
-## [Setup Page](/SetupJS.md/)
+## [Setup Page](SetupJS.md)
 #### GetAvailableCollections.js
+Contains function to retrieve all collections that are available to be inventoried at the selected location.
 #### GetSelectedCollections.js
+Will retrieve all collections selected to be inventoried in a session.
 #### AddCollection.js
+Will select one of the available collections to be included in an inventory session.
 #### RemoveCollection.js
+Will remove a collection from the list selected to be inventoried. 
 #### SaveSetup.js
+Saves the inventory setup, all of the selected collections.
 
-## [Scan Page](/ScanJS.md/)
+## [Scan Page](ScanJS.md)
 #### GetScanned.js
+Will retrieve previously scanned items present on the scan page.
 #### ScanBarcode.js
+Will insert a barcode into the input field and submit that code. 
 #### FinishScan.js
+Calls the internal function of the Scan Page to finish a scan session.
 
-## [Error Page](/ErrorJS.md/)
+## [Error Page](ErrorJS.md)
 #### GetError.js
-#### GoToScan.js
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+Will retrieve the message triggered by a item scan error. 
+#### GoToScan.js
+Advances from the error page to go back to the scan page.
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