Cleanup and textual review of userguide CH01-CH07

I've performed a review of chapters 1 through 7 of the userguide. 

Most of these are textual improvements, adding more flow to sentences, fixing typos, etc. I've also added the odd remark to clarify some things, removed a duplicate new section on logging from version 5.12 onwards and corrected some references to the old distribution which no longer match the download structure users will find.