OrganizeFoldersRename.jsx

<javascriptresource>
  <name>Organize Folders and Rename</name>
  <about>
      This will color code nested folders to help readiblity.
      It will also rename layers.
      - Evan Viera
  </about>
  <menu>filter</menu>
  <category>Viera</category>
  <type>automate</type>
  <enableinfo>true</enableinfo>
  </javascriptresource>

#include "vieraLibrary.jsx"

var doc = activeDocument;
var idColors = [ "Rd  ", "Orng", "Ylw ", "Grn ", "Bl  ", "Vlt ", "Gry " ];
var lastColor = 0;
var groupNum = 0;

colorGroupTags( doc );

//	****************************************
// 	Collects all layers underneat into array
//	****************************************
function colorGroupTags( __parent )
{
    var refLayer = new RegExp( /_REF_/gim );

    for ( var i = 0; i < __parent.layers.length; i++ )
    {
      var currentLayer = __parent.layers[ i ];
      var visible = currentLayer.visible;

      if ( !currentLayer.name.match( refLayer ) )
      {
        if ( currentLayer.typename == "ArtLayer" )
        {
          currentLayer.name = "LYR_" + i; // + "_" + currentLayer.blendMode;
        }
        else
        {
    			doc.activeLayer = currentLayer;
    			setLabelColor( idColors[ lastColor ] );
    			lastColor = (lastColor + 1) % idColors.length;
    			currentLayer.name = "GRP_" + groupNum;
          groupNum++;

          colorGroupTags( currentLayer );
        }
      }

      currentLayer.visible = visible;
    }
}