> BUT THE FOLDER THAT NEED AUTHENTICATION IS: 
> <http://harrisons.accessmedicine.com/server-java/>

Remember that httrack will never, by default, go outside 
the starting domain and/or go upper in the directory 
structures. You have to use filters (set options / scan 
rules) to let it go ; with a filter like:
+harrisons.accessmedicine.com/server-java/*

BTW, if you have many java classes, note that java is not 
totally well handled by httrack (there might be missing 
files, depending on the class structure)