diff --git a/lib/config/DocProcessor/docProcessor.js b/lib/config/DocProcessor/docProcessor.js
index d408e409d5..4fb795b541 100644
--- a/lib/config/DocProcessor/docProcessor.js
+++ b/lib/config/DocProcessor/docProcessor.js
@@ -23,9 +23,9 @@ function initPhase(aggData) {
 }
 
 
-function readPhase(srcFolder, filenames, aggData) {
+function readPhase(filenames, aggData) {
     for (var i = 0; i < filenames.length; i++) {
-        var pathname = path.resolve(srcFolder, filenames[i]);
+        var pathname = filenames[i];//path.resolve(srcFolder, filenames[i]);
         
         var src = fs.readFileSync(pathname);
         var tree = remark().use(frontMatter, ["yaml"]).parse(src);
@@ -46,9 +46,9 @@ function aggPhase(aggData) {
 }
 
 
-function updatePhase(srcFolder, destFolder, filenames, aggData) {
+function updatePhase(filenames, aggData) {
     for (var i = 0; i < filenames.length; i++) {
-        var pathname = path.resolve(srcFolder, filenames[i]);
+        var pathname = filenames[i]; // path.resolve(srcFolder, filenames[i]);
         
         var src = fs.readFileSync(pathname);
         var tree = remark().use(frontMatter, ["yaml"]).parse(src)
@@ -60,8 +60,9 @@ function updatePhase(srcFolder, destFolder, filenames, aggData) {
         });
         
         if (modified)
-            fs.writeFileSync(path.resolve(destFolder, filenames[i]), remark().use(frontMatter, {type: 'yaml', fence: '---'}).data("settings", {paddedTable: false}).stringify(tree));
-            //console.log(JSON.stringify(tree));
+            fs.writeFileSync(filenames[i], remark().use(frontMatter, {type: 'yaml', fence: '---'}).data("settings", {paddedTable: false}).stringify(tree));
+        
+        //console.log(JSON.stringify(tree));
     }
 }
 
@@ -91,8 +92,24 @@ function loadToolConfig(configFilePath) {
 }
 
 
+function getAllDocFilePaths(docFolder, files) {
+    var items = fs.readdirSync(docFolder);
+
+    for (var i = 0; i < items.length; i++) {
+        var itemPath = path.resolve(docFolder, items[i]);
+        var itemInfo = fs.statSync(itemPath);
+
+        if (itemInfo.isFile()){
+            files.push(itemPath);
+        } else if (itemInfo.isDirectory()) {
+            getAllDocFilePaths(itemPath, files);
+        }
+    }
+}
+
+
 program
-.usage("[options] <source> [dest]")
+.usage("[options] <source>")
 .parse(process.argv);
 
 if (program.args.length === 0) {
@@ -104,6 +121,7 @@ if (program.args.length === 0) {
 var sourcePath = path.resolve(program.args[0]);
 var sourceInfo = fs.statSync(sourcePath);
 
+/*
 var destPath;
 var destInfo;
 
@@ -119,19 +137,21 @@ if (sourceInfo.isDirectory() && !destInfo.isDirectory()) {
     console.log("Error: The <dest> argument must be a directory");
     return 0;
 }
+*/
 
 var toolModules = loadToolModules();
 var toolList = loadToolConfig(path.resolve(__dirname, configFileName));
 
 
-var files;
+var files = [];
 
 if (sourceInfo.isDirectory()) {
-    files = fs.readdirSync(sourcePath);
+    getAllDocFilePaths(sourcePath, files);
 } else if (sourceInfo.isFile()) {
-    files = [ path.basename(sourcePath) ];
-    sourcePath = path.dirname(sourcePath);
-    destPath = path.dirname(destPath);
+    files = [ sourcePath ];
+    //files = [ path.basename(sourcePath) ];
+    //sourcePath = path.dirname(sourcePath);
+    //destPath = path.dirname(destPath);
 }
 
 files = files.filter(filename => 
@@ -145,13 +165,13 @@ console.log("Initialising...");
 initPhase(aggData);
 
 console.log("Analysing Markdown files...");
-readPhase(sourcePath, files, aggData);
+readPhase(files, aggData);
 
 console.log("Computing aggregate data...");
 aggPhase(aggData);
 
 console.log("Updating Markdown files...");
-updatePhase(sourcePath, destPath, files, aggData);
+updatePhase(files, aggData);
 
 
 
diff --git a/lib/config/DocProcessor/tools/index.js b/lib/config/DocProcessor/tools/index.js
index 1b010edcde..38462ebe29 100644
--- a/lib/config/DocProcessor/tools/index.js
+++ b/lib/config/DocProcessor/tools/index.js
@@ -39,7 +39,7 @@ function initPhase(aggData) {
     aggData.srcData = {};
     aggData.mdFileDesc = [];
     aggData.mdFileStatus = [];
-
+    aggData.mdFilePath = [];
     searchLibraryRecursive(aggData.srcData, path.resolve(rootFolder));
 
     //console.log(JSON.stringify(aggData.srcData));
@@ -50,7 +50,7 @@ function readPhase(tree, pathname, aggData) {
     var itemName = path.basename(pathname, ".md");
 
     // Look for the first paragraph in the file by skipping other items.
-    // Should usually be a position 1 in the tree.
+    // Should usually be at position 1 in the tree.
     var s;
     var briefDesc;
 
@@ -80,6 +80,10 @@ function readPhase(tree, pathname, aggData) {
         }
 
     }
+
+    var linkPath = pathname.replace(/\\/g, '/');
+    linkPath = linkPath.substr(linkPath.indexOf("docs") + 5);
+    aggData.mdFilePath[itemName] = linkPath;
 }
 
 function aggPhase(aggData) {
@@ -159,6 +163,7 @@ function prepareIndexSections(aggData) {
         var briefDesc = aggData.mdFileDesc[itemName];
 
         var displayName = ngHelpers.ngNameToDisplayName(itemName);
+        var pathname = aggData.mdFilePath[itemName];
 
         var status = "";
 
@@ -169,6 +174,7 @@ function prepareIndexSections(aggData) {
             sections[libName][srcData.type].documented.push({
                 "displayName": displayName,
                 "mdName": itemName + ".md",
+                "mdPath": pathname,
                 "srcPath": srcData.path,
                 "briefDesc": briefDesc,
                 "status": status
@@ -280,7 +286,7 @@ function makeMDUndocumentedListItem(docItem) {
 
 
 function makeMDDocumentedTableRow(docItem) {
-    var mdFileLink = unist.makeLink(unist.makeText(docItem.displayName), docItem.mdName);
+    var mdFileLink = unist.makeLink(unist.makeText(docItem.displayName), docItem.mdPath);
     var srcFileLink = unist.makeLink(unist.makeText("Source"), "../lib/" + docItem.srcPath);
     var desc = docItem.briefDesc;
 
diff --git a/lib/config/DocProcessor/tools/versionIndex.js b/lib/config/DocProcessor/tools/versionIndex.js
index a67df3f5c5..50ed416a3d 100644
--- a/lib/config/DocProcessor/tools/versionIndex.js
+++ b/lib/config/DocProcessor/tools/versionIndex.js
@@ -31,7 +31,7 @@ function initPhase(aggData) {
 
 
 function readPhase(tree, pathname, aggData) {
-    var compName = path.basename(pathname, ".md");
+    var compName = pathname; //path.basename(pathname, ".md");
     var angNameRegex = /([a-zA-Z0-9\-]+)\.((component)|(directive)|(model)|(pipe)|(service)|(widget))/;
 
     if (!compName.match(angNameRegex))
@@ -86,13 +86,20 @@ function aggPhase(aggData) {
     for (var i = 0; i < keys.length; i++) {
         var version = keys[i];
         var versionItems = aggData.versions[version];
-        versionItems.sort();
+        versionItems.sort((a, b) => {
+            var aa = path.basename(a, ".md");
+            var bb = path.basename(b, ".md");
+
+            return aa.localeCompare(bb);
+        });
 
         var versListItems = [];
 
         for (var v = 0; v < versionItems.length; v++) {
-            var displayName = ngHelpers.ngNameToDisplayName(versionItems[v]);
-            var pageLink = versionItems[v] + ".md";
+            var displayName = ngHelpers.ngNameToDisplayName(path.basename(versionItems[v], ".md"));
+            var pageLink = versionItems[v];// + ".md";
+            pageLink = pageLink.replace(/\\/g, '/');
+            pageLink = pageLink.substr(pageLink.indexOf("docs") + 5);
 
             versListItems.push(
                 unist.makeListItem(