Hopefully this will finally fix the merging issues I had.

ScriptUI Panels/yToolBox.jsx

@@ -1,3 +1,4 @@
+<<<<<<< HEAD
 var scriptUIPanel = this;
 YTB =
 {   
@@ -122,3 +123,6 @@ YTB.init();
 #include "../yScripts/y_CPOffset.jsx";
 #include "../yScripts/y_puppetRig.jsx";
 #include "../yScripts/y_stopMotionLayer.jsx";
+=======
+var scriptUIPanel = this;␍YTB =␍{   ␍    info :␍    {␍        name : "yToolBox",␍        ver : 0.5,␍        status : "alpha",␍        url : "yorchnet.com",␍        description : "My mixed bag of tools"␍    },␍    resources :␍    {␍        icon : new File('../yScripts/yNet.png'),␍        header :  new File('../yScripts/header.png')␍    },␍    appearence :␍    {␍      buttonHeight : 30,␍      buttonWidth : 126  ␍    },␍    tools : [],␍    createUI : function createUI()␍    {␍        var res ="group\␍        {\␍        orientation:'column',\␍        alignment:['fill','fill'],\␍        margins:[0,0,0,0]\␍        header: Group\␍        {\␍            orientation:'column',\␍            alignment:['center','top'],\␍            margins:[0,0,0,0]\␍            title: Image\␍            {\␍                icon:'" + this.resources.header.path + '/' + this.resources.header.name + "',\␍                preferredSize: [175, 35]},\␍                ver: StaticText\␍                {\␍                    text:'" + this.info.ver + "',\␍                    alignment:['center','center']\␍                }\␍                desc: StaticText\␍                {\␍                    text:'" + this.info.description + "',\␍                    alignment:['center','center']\␍                },\␍        },\␍        main: Group\␍        {\␍            orientation:'column',\␍            alignment:['fill','fill'],\␍            alignChildren:['center','center'],\␍        },\␍        footer: Group\␍        {\␍        alignment:['center','bottom'], \␍                icn_app: Image {icon:'" + this.resources.icon.path + '/' + this.resources.icon.name + "',preferredSize: [15, 18]},\␍                txt_info: StaticText { text:'"+ this.info.url + "', alignment:['fill','center'] },\␍            }, \␍        }";␍        this.window.grp = this.window.add( res );␍        ␍        this.window.layout.layout(true);␍        this.customizeUI();␍        ␍        //EventHandlerAssignment␍        this.window.onResize = this.resize;␍        this.window.onClose = this.close;␍        this.window.onDraw = this.autoLayout;␍    },␍    customizeUI : function customizeUI()␍    {␍        var g  = this.window.graphics;    ␍        var orange = g.newBrush(g.BrushType.SOLID_COLOR, [1, .45, 0, 1]);    ␍        this.window.grp.main.graphics.backgroundColor = orange;␍    },␍    addTool : function addTool( aTool )␍    {␍        /**** TO DO ****/␍        // Check that the tool object is unique.␍        // Call for a window resize so it refreshes propperly.␍        ␍        this.tools.push( aTool );␍␍        var btn  = this.window.grp.main.add( aTool.btnLauyout );␍        ␍        btn.onClick = aTool.activate;␍        btn.yTool = aTool; // add a reference to the tool so I can access info on it later...␍        ␍        //alert(btn.onClick);␍␍        this.window.layout.layout(true);␍        ␍    },␍    //EVENT HANDLERS␍    resize : function resize()␍    {␍        this.layout.resize();␍    },␍    close : function close()␍    {␍        YTB = null;␍        delete this;␍    },␍    init : function init()␍    {␍        this.window = ( scriptUIPanel instanceof Panel ) ? scriptUIPanel: new Window( "palette" , this.info.name , undefined, { resizeable : true } );␍        this.createUI();␍    }␍    ␍};␍␍YTB.init();␍␍#include "../yScripts/y_setStructure.jsx";␍#include "../yScripts/y_colorProbe.jsx";␍#include "../yScripts/y_BindBetween2.jsx";␍#include "../yScripts/y_CPOffset.jsx";␍#include "../yScripts/y_puppetRig.jsx";␍#include "../yScripts/y_GenericNewScript.jsx";
+>>>>>>> 84e17ed... Adapted all scripts to work on their own and with the toolbox.

yScripts/y_BindBetween2.jsx

@@ -93,7 +93,7 @@ function YBindBetween2()
     }
     this.activate = function activate()
     {
-	this.yTool.yMainFunction();
+        yBindBetween2.yMainFunction();
     }
     this.run = function run()
     {
@@ -212,5 +212,5 @@ if (typeof(YTB)=='undefined')
 }
 else
 {
-    YTB.addTool(new YBindBetween2());
+    yBindBetween2 = YTB.addTool(new YBindBetween2());
 }

yScripts/y_colorProbe.jsx

@@ -63,7 +63,7 @@ function YColorProbe()
     }
     this.yMainFunction = function yMainFunction()
     {
-	app.beginUndoGroup(this.yTool.info.name); // yTool is a refernece to the Tool object, because THIS in this context returns the ButtonObject.... 
+	app.beginUndoGroup( yColorProbe.info.name ); // yTool is a refernece to the Tool object, because THIS in this context returns the ButtonObject.... 
 	
 	//It works with Sampled layers at a 100% scale only.
 	try
@@ -124,5 +124,5 @@ if (typeof(YTB)=='undefined')
 }
 else
 {
-    YTB.addTool(new YColorProbe());
+    yColorProbe = YTB.addTool(new YColorProbe());
 }

yScripts/y_puppetRig.jsx

@@ -4,9 +4,9 @@ function YPuppetRigTool()
     this.info =
     {
 	name : "yPuppetRig",
-	version : 0.33,
+	version : 0.0,
 	stage : "development",
-	description : "Tools for streamlining puppet-based animation rigs.",
+	description : "Tool to create nulls at puppet pin locations, and link the latter to the former.",
 	url : "yorchnet.com"
     };
     this.appearence =
@@ -98,7 +98,7 @@ function YPuppetRigTool()
     }
     this.activate = function activate()
     {
-	this.yTool.yMainFunction();
+        yPuppetRigTool.yMainFunction();
     }
     
     /**/