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();
     }
     
     /**/