Update_Docs: Initial Work to Allow Subdirectory Scanning

The changes are not as widespread as it appears, but a large percentage of the code had to be indented

Doesn't fully work yet.
Update_Docs: Print SubDir Files in Items and Modules List
Update_Docs: Move Package Sorting Outside of Directory Loop

This allows for sorting of the entire list, not just parts of it
Update_Docs: Fix Regex Error Used to Distinguish Items from Modules

"sub new" should be followed by a whitespace character, but no necessarily a space
Update_Docs: Disable code which deleted files in the distro dir; Cleanup internal comments

Script previously would delete extra files in the /doc dir even when users had followed the suggested install procedure and used an alternative docs dir.  The distribution directory structure should not be modified if users are installing things the way we suggest.
Format Docs: Make Head3 Larger, Add Head4 Style

It looked silly to have heading 3 smaller than the body text.
Heading4 is not often used, but it should be defined to avoid the default setting in browsers.
Update Docs: Fix Pod2Html Commands so Links Are Created; Modify Example.pod

The settings in pod2html were preventing proper links from being created.  The new settings allow it to properly search the pod directories

Updated Example.pod to suggest using a link to identify inherited objects.
Merge pull request #220 from krkeegan/update_docs

Enable Update_Docs to Scan Subdirectories; Stop Deleting Distro Files; Fix Docs CSS