lilypond-manuals.css: edit color scheme and some spacing

Simplifies the color scheme. Main motivation is to avoid fully
saturated bright colors on code box borders, which distract from
the content, and to use stronger/darker colors in table of
contents sidebars instead of lighter pastel colors.

Affects table of contents sidebars, borders around code boxes,
footers, note boxes, advanced boxes, main/top page for a manual,
and grey navigation bars/rows/strips.