Fix Issue #113: Fix die issue when updating docs

Original code would create fake .pm entries in %libfiles while checking if .pm or .pl file exists.  This combined with a "or Die()" line in the next section of code caused the update to abort after processing one new .pl file.  Subsequent calls would again process one .pl file until eventually (if called every day) finishing all the .pl files. Also fixed ambiguous use of --htmldir and --htmlroot; man page says only one should be specified.
Merge pull request #115 from mstovenour/fix_issue_113

Fix Issue #113: Fix die issue when updating docs