Line Overflow and Page Breaks in References (Bibliography in RMarkdown PDF Pandoc)

Question

Update

I rewrote the post providing a MWE according to the suggestions by the comments below.

Problem

When generating the list of references at the end of my paper, the PDF output has two issues which I can't solve.

1) Links overflow page border but should get a page break at the dash.

2) Bibliography items are split across pages but should stay as one block.

My Document

I'm using RMarkdown with Pandoc to generate a PDF based on http://rmarkdown.rstudio.com/authoring_pandoc_markdown.html#citations

According to the documentation, the list of references is placed at the end of the document. So, I don't have anything like \printbibliography or so.

Using 'knit pdf' in RStudio seems to execute:

/Applications/RStudio.app/Contents/MacOS/pandoc/pandoc +RTS -K512m -RTS MWE.utf8.md 
--to latex 
--from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash 
--output MWE.tex 
--template /usr/local/lib/R/3.3/site-library/rmarkdown/rmd/latex/default-1.15.2.tex 
--highlight-style tango 
--latex-engine /Library/TeX/texbin/xelatex 
--variable graphics=yes 
--bibliography library.bib 
--filter /Applications/RStudio.app/Contents/MacOS/pandoc/pandoc-citeproc

MWE.Rmd

---
output: 
  pdf_document:
    latex_engine: xelatex
    keep_tex: true
bibliography: library.bib
fontsize: 12pt
geometry:
  margin = 1.2in,
  paper = a4paper,
  inner = 1.5cm,
  bindingoffset = 2cm,
  outer = 2cm,
  top = 2.5cm,
  bottom = 2.5cm
header-includes:
- \usepackage{setspace}
- \usepackage{lipsum}
- \onehalfspacing
---

#  Content

@Boner2015 states that...

I need another line...

And another...

\lipsum[1-3]

# References

\setlength{\parindent}{-0.2in}
\setlength{\leftskip}{0.2in}
\setlength{\parskip}{8pt}
\noindent

library.bib

@misc{Boner2015,
author = {Bon{\'{e}}r, Jonas},
title = {{Interview with Tony Rae Moore: Typesafe AMA Podcast Ep. 03 feat. How Akka Actors Help Build Microservices with Jonas Bon{\'{e}}r}},
url = {https://www.lightbend.com/blog/typesafe-ama-podcast-ep-03-feat-akka-actors-microservices-jonas-boner},
urldate = {2016-11-22},
year = {2015}
}

Generated MWE.tex

\documentclass[12pt,]{article}
\usepackage{lmodern}
\usepackage{amssymb,amsmath}
\usepackage{ifxetex,ifluatex}
\usepackage{fixltx2e} % provides \textsubscript
\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
  \usepackage[T1]{fontenc}
  \usepackage[utf8]{inputenc}
\else % if luatex or xelatex
  \ifxetex
    \usepackage{mathspec}
  \else
    \usepackage{fontspec}
  \fi
  \defaultfontfeatures{Ligatures=TeX,Scale=MatchLowercase}
  \newcommand{\euro}{â¬}
\fi
% use upquote if available, for straight quotes in verbatim environments
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
% use microtype if available
\IfFileExists{microtype.sty}{%
\usepackage{microtype}
\UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
}{}
\usepackage[margin = 1.2in, paper = a4paper, inner = 1.5cm, bindingoffset = 2cm,
outer = 2cm, top = 2.5cm, bottom = 2.5cm]{geometry}
\usepackage{hyperref}
\PassOptionsToPackage{usenames,dvipsnames}{color} % color is loaded by hyperref
\hypersetup{unicode=true,
            pdfborder={0 0 0},
            breaklinks=true}
\urlstyle{same}  % don't use monospace font for urls
\usepackage{graphicx,grffile}
\makeatletter
\def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
\def\maxheight{\ifdim\Gin@nat@height>\textheight\textheight\else\Gin@nat@height\fi}
\makeatother
% Scale images if necessary, so that they will not overflow the page
% margins by default, and it is still possible to overwrite the defaults
% using explicit options in \includegraphics[width, height, ...]{}
\setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio}
\setlength{\parindent}{0pt}
\setlength{\parskip}{6pt plus 2pt minus 1pt}
\setlength{\emergencystretch}{3em}  % prevent overfull lines
\providecommand{\tightlist}{%
  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
\setcounter{secnumdepth}{0}

%%% Use protect on footnotes to avoid problems with footnotes in titles
\let\rmarkdownfootnote\footnote%
\def\footnote{\protect\rmarkdownfootnote}

%%% Change title format to be more compact
\usepackage{titling}

% Create subtitle command for use in maketitle
\newcommand{\subtitle}[1]{
  \posttitle{
    \begin{center}\large#1\end{center}
    }
}

\setlength{\droptitle}{-2em}
  \title{}
  \pretitle{\vspace{\droptitle}}
  \posttitle{}
  \author{}
  \preauthor{}\postauthor{}
  \date{}
  \predate{}\postdate{}


\usepackage{setspace}
\usepackage{lipsum}
\onehalfspacing

% Redefines (sub)paragraphs to behave more like sections
\ifx\paragraph\undefined\else
\let\oldparagraph\paragraph
\renewcommand{\paragraph}[1]{\oldparagraph{#1}\mbox{}}
\fi
\ifx\subparagraph\undefined\else
\let\oldsubparagraph\subparagraph
\renewcommand{\subparagraph}[1]{\oldsubparagraph{#1}\mbox{}}
\fi

\begin{document}

\section{Content}\label{content}

Bonér (2015) states that\ldots{}

I need another line\ldots{}

And another\ldots{}

\lipsum[1-3]

\section{References}\label{references}

\setlength{\parindent}{-0.2in} \setlength{\leftskip}{0.2in}
\setlength{\parskip}{8pt} \noindent

\hypertarget{refs}{}
\hypertarget{ref-Boner2015}{}
Bonér, Jonas. 2015. ``Interview with Tony Rae Moore: Typesafe AMA
Podcast Ep. 03 Feat. How Akka Actors Help Build Microservices with Jonas
Bonér.''
\url{https://www.lightbend.com/blog/typesafe-ama-podcast-ep-03-feat-akka-actors-microservices-jonas-boner}.

\end{document}

Answer 1

For issue 1, I added the following under header-includes:

\def\UrlBreaks{\do\/\do-\do?}

It adds additional characters on which the url can break, which can be done while hypperref is already loaded, apparently.

The solution for issue 2 is not doing it for me.

Answer 2

Thanks to @jon and @moewe, issue 1 can be resolved by putting \PassOptionsToPackage{hyphens}{url} before loading hyperref (\usepackage{hyperref}). In my case that was not possible in the header-include: of the RMarkdown YAML because it uses some default .tex file where hyperrefis already loaded. For me, it is okay to modify the default .text file.

Regarding issue 2, apparently RMarkdown with Pandoc and CSL generates paragraphs (separated by an empty line) for each bibliography item of the following format

\hypertarget{ref-Boner2015}{}
Bonér, J. (2015). \emph{Interview with Tony Rae Moore: Typesafe AMA
Podcast Ep. 03 feat. How Akka Actors Help Build Microservices with Jonas
Bonér}. {[}Online{]}. Available from:
\url{https://www.lightbend.com/blog/typesafe-ama-podcast-ep-03-feat-akka-actors-microservices-jonas-boner}.
{[}Accessed: 22 November 2016{]}.

Usually, according to How to avoid page-breaks inside paragraphs? this would work:

\widowpenalties 1 10000
\raggedbottom

But, having \hypertarget prevents page breaks (Multiple \hypertarget overflow the page?). Therefore, in addition, I had to place a \leavevmode in front of every \hypertarget resulting in overwriting \hypertarget:

\usepackage{letltxmacro}
\LetLtxMacro{\oldhypertarget}{\hypertarget}
\renewcommand{\hypertarget}[2]{\leavevmode\oldhypertarget{#1}{#2}}