Update documentation to new style.

o Stylesheet is in manual.css.
o Most files had to have html adjustments. (<pre> --> <code>)
o Only very minor content changes.
dos2unix
Add paragraph tags.

Some minor reformatting too.
add anchors for each section of user manuals
Add section header anchors.

* origin/pull/1/head:
  add anchors for each section of user manuals
Merge pull request #378 from batrick/manual-update

Manual Style Update