Dikla,
Working with the minified code that you get when downloading from a AGOL WAB app can be difficult but most of what you want to do is CSS so its not to bad. But as Rebecca points out if you are going to want and modify yours apps in the future then you need to get the WAB Dev version.
1a. In the main config.json file make these changes (change the top attribute):
a.{"uri":"themes/JewelryBoxTheme/widgets/HeaderController/Widget","position:{"left":0,"top":0,"right":0,"height":60,"relativeTo":"browser"}
b. {"visible":false,"panel":{"uri":"themes/JewelryBoxTheme/panels/LDockablePanel/Panel","position":{"left":0,"top":60,"bottom":0,"width":360,"relativeTo":"browser"}}
c. "map":{"3D":false,"2D":true,"position":{"left":0,"top":60,"right":0,"bottom":0}
I have change them all to 60 as an example.
1b. In the \themes\JewelryBoxTheme\widgets\HeaderController\Widget.js make these change to allow for a larger logo
(Search for the following lines and make your adjustment to the 30 number(s)):
a. .logo{*/ height: 30px;}
b. _setElementsSize:function(){a.setStyle(this.logoNode,{height:"30px",marginTop:(this.height-30)/2+"px"});a.setStyle(this.titleNode,{lineHeight:this.height+"px"});
2. In the \jimu.js\css\jimu-theme.css (change both the bold sections)
.jimu-main-background{background-color: #485566; background-color: rgba(72, 85, 102, 0.9);}
3. In the main config.json search for the following text (exactly) and delete it:
,{"uri":"widgets/LayerList/Widget","version":"2.0","id":"widgets_LayerList_Widget_17","name":"LayerList","label":"Layer List","index":1}
