Fix whitespace
Rework warning boxes

The number of warning boxes was becoming somewhat
overwhelming. Before adding another one, I restructured
the intro to allow an entire "prep checklist".
Add search re-indexing item
Alphabetize checklist
Add win-config section
simplify wording for search re-index
Merge pull request #728 from joshmoore/rebased/develop/5.0.1-upgrade

5.0.1 upgrade additions. (rebased onto develop)