Fix broken links [nextstrain/docs.nextstrain.org#14]

* Link to "community page on site" rather than "community section on
  front page"
* Update colorbrewer link to HTTPS
* Update link to Zika reference GenBank file to current location in
  repo
* Update link to example that was removed from the repo to point to
  last version before deletion

docs/examples/examples.rst

@@ -45,4 +45,4 @@ Nextstrain community
 ====================
 
 Nextstrain also provides access to analyses by independent groups `stored and accessed via public GitHub repos <https://nextstrain.org/docs/contributing/community-builds>`__, all of which currently use augur.
-For the most up-to-date listing of these please see the `community section on the nextstrain front page. <https://nextstrain.org/#community>`__
+For the most up-to-date listing of these please see the `community section on the nextstrain site. <https://nextstrain.org/community>`__

docs/faq/colors.md

@@ -20,7 +20,7 @@ country	american samoa	#3F50CC
 country	fiji	#3F5ED0
 ```
 
-The hexadecimal notation starts with a #, followed by two letters coding for red, green, blue values. If you need advice or inspiration for colors, have a look at [colorbrewer](http://colorbrewer2.org/#type=sequential&scheme=BuGn&n=3).
+The hexadecimal notation starts with a #, followed by two letters coding for red, green, blue values. If you need advice or inspiration for colors, have a look at [colorbrewer](https://colorbrewer2.org/#type=sequential&scheme=BuGn&n=3).
 Pay particular not to mix tabs and spaces for column separation.
 The line
 ```

docs/faq/import-beast.md

@@ -66,4 +66,8 @@ augur import beast --mcc data/beast.mcc.nex --output-tree results/mers.new
     --most-recent-tip-date 2018.43
 ```
 
-A full [example build can be found here](https://github.com/nextstrain/augur/tree/master/tests/builds/beast_mers).
+A full [example build can be found here][]. (N.b., this build has been
+removed from the current version of the repository; the link here is
+to the last version prior to its removal.)
+
+[example build can be found here]: https://github.com/nextstrain/augur/blob/73b8a71103bae3a36b49acdee7c7c75a7e69a751/tests/builds/beast_mers/Snakefile

docs/faq/translate_ref.md

@@ -30,12 +30,12 @@ Augur will only translate genes which have 'CDS' as the feature name, and have a
                      /gene="ENV"
 ```
 
-Compare the [original Zika reference on Genbank](https://www.ncbi.nlm.nih.gov/nuccore/KX369547) to the [one used on Nextstrain](https://github.com/nextstrain/zika/blob/master/config/zika_reference.gb). Notice that the genes are designated by `CDS` instead of `mat_peptide` and have an entry for `/gene=` as well as `/product=`.
+Compare the [original Zika reference on Genbank](https://www.ncbi.nlm.nih.gov/nuccore/KX369547) to the [one used on Nextstrain](https://github.com/nextstrain/zika/blob/-/phylogenetic/defaults/zika_reference.gb). Notice that the genes are designated by `CDS` instead of `mat_peptide` and have an entry for `/gene=` as well as `/product=`.
 
 ### VCF
 
 You can also find an appropriate GFF annotation reference on GenBank. Be sure to pick one that is very close to the strain you are using - especially if there might be variability in the genes present! If the positions in the GFF file do not match the positions in your VCF file, it will not work.
 
 To download a file from GenBank, use the 'send to' button in the top-right corner, then select 'Complete Record', 'File', and 'GFF3' for the format.
 
-You will have to modify the first column of the GFF so that it matches the `CHROM` (first column) of your VCF file.
+You will have to modify the first column of the GFF so that it matches the `CHROM` (first column) of your VCF file.