update: styles for code blocks

[atusy]

This PR improves styles for code blocks.

html_document2 / html_chapter / html_book

This part is related to #733 and #706.

When Pandoc's syntax highlighting is enabled and clean_highlight_tags: TRUE, Pandoc embeds CSS and cause code blocks to have no margins. Exceptionally, the matter does not happen when highlight: default in html_document2

div.sourceCode { margin: 1em 0; }
pre.sourceCode { margin: 0; }

For the html_document2, Pandoc embeds CSS starting from <style type="text/css" data-origin="pandoc">.
Thus, I decided to remove unwanted styles by updating clean_pandoc2_tags.

For the others, Pandoc embeds CSS starting from <style type="text/css">, which cannot be telled if the CSS is added by Pandoc or the user.
Thus, I decided to add CSS to template (default.html) to override the one embedded by Pandoc.
I also updated CSS in the similar way as rstudio/rmarkdown#1596, so that output code blocks have white background when line numbering is enabled.

Before

After

html_gitbook

When line nubering is enabled for code blocks, they are positioned too left, and may overflow.
Thus I updated html_gitbook's template.

Before

After

Source code for examples above

The above output is rendered from the source code below with

• latest knitr on GitHub
• Update stylesheet for code blocks with line-numbers rmarkdown#1596

---
output: 
  bookdown::html_book: 
    highlight: default
  bookdown::html_document2:
    highlight: tango
  bookdown::gitbook: 
    highlight: tango
---

Numbered

```{r hello, class.source = "numberLines", class.output="numberLines", attr.output='startFrom="10"'}
"Hello World"
```

Unnumbered

```{r hello2}
"Hello World"
```

[atusy]

For the html_document2, Pandoc embeds CSS starting from <style type="text/css" data-origin="pandoc">.
Thus, I decided to remove unwanted styles by updating clean_pandoc2_tags.

This approach can be vulnerable to the updates of Pandoc.
Another solution is to add external CSS by using htmltools::html_dependency.
However, this makes output html complex and heavier.
Updating the template is not preferred because html_document2 shares the template with rmarkdown::html_document.

[atusy]

I close this PR and come back late because I want some rethinking.

• For html_document2, 52b71f9 removed clean_pandoc2_highlight_tags
• For html_book and gitbook, I feel I have better places to embed additional CSS

[yihui]

Instead of enumerating all classes with the CSS selector [] (which seems to be cumbersome), will something like .numberLines work?

[atusy]

I agree this seems to be cumbersome.
However, if

pre.numberLines { background-color: white; }

is applied, then we cannot use chunk option and bootstrap's CSS (e.g., output.classs='.bg-warning') to change background color of output.

https://github.com/yihui/knitr-examples/blob/b6937427954e4bceafd9a112237d1aa80215cd2d/116-html-class.Rmd#L16