display and formatting stuff

[owainevans]

1. numbered lists (including table of contents and footnotes) should have regular numerals instead of roman ones.
2. there should be a default footer with a header for footnotes "## Foonotes" (see example in 5a), a heading for references, and then links to previous chapter, next chapter and table contents.
3. the table of contents page should have the form "section header" (no link) and then each chapter in section. instead of current setup where the section header is always a link to a chapter.