title: Bookdown: Chapter/Section cross referencing not working (gitbook)
body: <p>I was having trouble with one of my bookdown projects where the chapter/section cross-references were no longer working in the html output. </p>
  
  <p>The problem is the html links work but they are displayed as <strong>??</strong> -- lacking section number.  This is only a problem in the html version of the book.  The pdf version compiles properly.</p>
  
  <p>In searching for a solution I tried creating a <em>new bookdown</em> project using the default demo install and it has the same error as highlighted in this image:</p>
  
  <p><img src="https://i.stack.imgur.com/LOF6N.png" alt="broken cross-reference in bookdown">.</p>
  
  <p>As noted -- this error is occurring in the default install of bookdown... 
  excerpt from the <code>01-intro.Rmd</code> (i.e. in Rstudio: File >> New Project >> New Directory >> Book project using bookdown).</p>
  
  <pre><code># Introduction {#intro}
  
  You can label chapter and section titles using `{#label}` 
  after them, e.g., we can reference Chapter \@ref(intro). 
  If you do not manually label them, there will be automatic labels anyway,
  e.g., Chapter \@ref(methods).
  
  Figures and tables with captions will be placed in `figure`
  and `table` environments, respectively.
  
  </code></pre>
  
  <p>Here is my <code>sessionInfo()</code></p>
  
  <pre class="lang-r prettyprint-override"><code>&gt; sessionInfo()
  R version 3.6.1 (2019-07-05)
  Platform: x86_64-w64-mingw32/x64 (64-bit)
  Running under: Windows 10 x64 (build 17134)
  
  Matrix products: default
  
  locale:
  [1] LC_COLLATE=English_United States.1252 
  [2] LC_CTYPE=English_United States.1252   
  [3] LC_MONETARY=English_United States.1252
  [4] LC_NUMERIC=C                          
  [5] LC_TIME=English_United States.1252    
  
  attached base packages:
  [1] stats     graphics  grDevices utils     datasets  methods   base     
  
  loaded via a namespace (and not attached):
   [1] compiler_3.6.1  bookdown_0.16   htmltools_0.4.0 tools_3.6.1    
   [5] yaml_2.2.0      Rcpp_1.0.3      rmarkdown_2.0   knitr_1.26     
   [9] xfun_0.11       digest_0.6.23   rlang_0.4.2     evaluate_0.14
  </code></pre>