I have been using WinHTTrack for a few years now to help users get files off a
protected site to share with their clients.  The files and links are created
dynamically by an analysis tool then the user can download the link with all
files.  

Recently it stopped capturing all files.  The link I paste is

<http://tlpa-pc.swg.usma.ibm.com/TLA_Reports/Customer_SomeClust2_2014-03-06_14~46~40_EST/>

I am now getting index.html and all direct links but none of the links
embedded in js - example:
document.write with href="Some_Long_File_Name_detail.html"