Remove unused includes
Ignore all zips in the downloads folder
Remove old 3.1 build PHP script
Remove comments link from standard footer sharedcode.
Trim the related links back down to only 4
Update Makefile "dist" target to also make a zip of only includes.
Remove unused sharedcode files
Update root ignore with some better wildcards
Update standard templates to remove "fixed" param

Also uses PHP and JSP functions for relative includes that don't need to
be routed through the SAPI.
Update the affilate templates to 4.0
Bump DEP version for "official" release
Merge branch '4.0' of github.com:unl/wdntemplates into 4.0