Fix various broken links [#1569]

Author: genehack

docs/faq/metadata.rst

@@ -81,8 +81,7 @@ locations ('new_zealand' became 'New Zealand').
 
 Auspice will still do this if you are exporting 'V1' type JSON files
 (from augur v5 or augur v6 using ``export v1``), but will not do this if
-you are using ``export v2`` (`read
-more <../releases/migrating-v5-v6.html#prettifying-metadata-fields>`__).
+you are using ``export v2`` (:ref:`read more <prettifying-metadata-fields>`).
 Instead, you should update your metadata files so that traits look the
 same as you'd like them to display in Auspice (change 'new_zealand' to
 'New Zealand' in your metadata, and in any additional latitude-longitude

docs/faq/what-is-a-build.md

@@ -11,7 +11,7 @@ These steps, taken together, are what we refer to as a "build".
 
 ### Example build
 
-The [Zika virus tutorial](https://docs.nextstrain.org/en/latest/tutorials/zika.html#build-steps) describes a build which contains the following steps:
+The [Zika virus tutorial](https://docs.nextstrain.org/en/latest/tutorials/creating-a-phylogenetic-workflow.html#run-a-nextstrain-build) describes a build which contains the following steps:
 
 1. Prepare pathogen sequences and metadata
 2. Align sequences
@@ -28,5 +28,5 @@ If you look at the [other tutorials](https://docs.nextstrain.org/en/latest/tutor
 While it is possible to run a build by running each of the individual steps, we typically group these together into a make-type file.
 [Snakemake](https://snakemake.readthedocs.io/en/stable/index.html) is "a tool to create reproducible and scalable data analyses... via a human-readable, Python-based language."
 
-> Snakemake is installed as part of the [conda environment](https://docs.nextstrain.org/en/latest/guides/install/local-installation.html#install-augur-auspice-with-conda) or the [docker container](https://docs.nextstrain.org/en/latest/guides/install/cli-install.html).
+> Snakemake is installed as part of the [conda environment](https://docs.nextstrain.org/en/latest/guides/install/local-installation.html) or the [docker container](https://docs.nextstrain.org/en/latest/guides/install/cli-install.html).
 If you ever see a build which has a "Snakefile" then you can run this by typing `snakemake --cores 1` or `nextstrain build --cpus 1 .`, respectively.

docs/usage/cli/export.rst

@@ -2,8 +2,7 @@
 augur export
 ============
 
-.. note:: The behavior of ``augur export`` has changed in v6. Please see `here <../../upgrading/migrating-v5-v6.html>`__ for more details.
-
+.. note:: The behavior of ``augur export`` has changed in v6. Please see :doc:`here <../../releases/migrating-v5-v6>` for more details.
 
 .. argparse::
     :module: augur

docs/usage/usage.rst

@@ -14,7 +14,7 @@ Each command requires at least one input file and will produce one or more outpu
 
 Most commands admit additional arguments to modify how the analysis is run.
 Each command is documented below, and we are continually adding more examples to each command and providing real-life examples of their usage.
-For instance, the documentation for `augur filter <./cli/filter.html>`__ shows how we use this to subsample the `nextstrain zika analysis <https://nextstrain.org/zika>`__.
+For instance, the documentation for :doc:`augur filter <./cli/filter>` shows how we use this to subsample the `nextstrain zika analysis <https://nextstrain.org/zika>`__.
 
 
 `Note that you can also run each command with the` ``--help`` `option, for example` ``augur tree --help``, `for more information at the command-line.`