[fetch-docs] update links

Update links according to URLs resulting from
the merging of nextstrain/docs.nextstrain.org#36

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

@@ -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/cli/doc/installation.html).
+> 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).
 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/index.rst

@@ -9,7 +9,7 @@ Augur: A bioinformatics toolkit for phylogenetic analysis
    The documentation you are viewing is Augur's reference guide, which means it is information-oriented and targeted at users who just need info about how Augur works.
 
    * If you have a question about how to achieve a specific goal with Augur, check out our :doc:`Augur-focused How-to Guides section <docs.nextstrain.org:guides/bioinformatics/index>` in the main Nextstrain documentation.
-   * If you want to learn the basics of how to use Augur from scratch, check out our :doc:`Zika tutorial <docs.nextstrain.org:augur/docs/tutorials/zika_tutorial>` in the main Nextstrain documentation.
+   * If you want to learn the basics of how to use Augur from scratch, check out our :doc:`Zika tutorial <docs.nextstrain.org:tutorials/zika_tutorial>` in the main Nextstrain documentation.
    * If you want to understand how Augur fits together with Auspice to visualize results, check out our :doc:`Data Formats section <docs.nextstrain.org:reference/formats/data-formats>` in the main Nextstrain documentation.
 
 

docs/releases/migrating-v5-v6.md

@@ -119,7 +119,8 @@ These may have been inferred for internal nodes by Augur functions like `augur t
 Certain traits have a geographic interpretation, e.g. "country".
 Auspice will attempt to display these traits on a map (and provide a drop-down to switch between them if there are more than one).
 
-> _Make sure that these have corresponding entry in the lat-longs TSV file supplied to `export`. See how to do this [here](https://docs.nextstrain.org/en/latest/augur/docs/faq/lat_longs.html)._
+> _Make sure that these have corresponding entry in the lat-longs TSV file supplied to `export`. See how to do this [here](https://docs.nextstrain.org/en/latest/guides/bioinformatics/lat_longs.html)._
+
 
 
 ---
@@ -528,5 +529,6 @@ In Auspice v2, all values are now displayed exactly as they arrive, allowing use
 
 Don't forget to also change them in any custom lat-long and/or coloring files you are using. We've also become stricter about the format of the files that pass in color and lat-long information. Previously, it didn't matter if columns were separated by spaces or tabs - now, they must be separated by tabs.
 
-You can find out more about how to add [custom coloring](https://docs.nextstrain.org/en/latest/augur/docs/faq/colors.html) and [lat-long](https://docs.nextstrain.org/en/latest/augur/docs/faq/lat_longs.html) values.
+You can find out more about how to add [custom coloring](https://docs.nextstrain.org/en/latest/guides/bioinformatics/colors.html) and [lat-long](https://docs.nextstrain.org/en/latest/guides/bioinformatics/lat_longs.html) values.
+
 If you use the command `parse` to generate a metadata table from fields in a fasta header, you can use the flag `--prettify-fields` to apply some prettifying operations to specific metadata entries, see the documentation [`parse`](/usage/cli/parse).

docs/releases/v6.md

@@ -46,7 +46,7 @@ Users can ask for this output and specify a file name using `--output-sequences`
 <span style='color: orange'>Deprecation warning:</span> The argument `--output` is now deprecated. Please use `--output-node-data` instead.
 
 ## Import BEAST MCC trees
-We now have instructions and functionality to import BEAST trees, see [here](https://docs.nextstrain.org/en/latest/augur/docs/faq/import-beast.html).
+We now have instructions and functionality to import BEAST trees, see [here](https://docs.nextstrain.org/en/latest/guides/bioinformatics/import-beast.html).
 
 ## Prettifying of strings
 Previous auspice version "prettified" metadata strings (like changing 'north_america' to 'North America').

docs/usage/cli/filter.rst

@@ -15,7 +15,7 @@ augur filter
 How we subsample sequences in the zika-tutoral
 ==============================================
 
-As an example, we'll look that the ``filter`` command in greater detail using material form the :doc:`zika tutorial <docs.nextstrain.org:augur/docs/tutorials/zika_tutorial>`.
+As an example, we'll look that the ``filter`` command in greater detail using material form the :doc:`zika tutorial <docs.nextstrain.org:tutorials/zika_tutorial>`.
 The filter command allows you to selected various subsets of your input data for different types of analysis.
 A simple example use of this command would be
 
@@ -45,7 +45,7 @@ To drop such strains, you can pass the name of this file to the augur filter com
              --output filtered.fasta
 
 (To improve legibility, we have wrapped the command across multiple lines.)
-If you run this command (you should be able to copy-paste this into your terminal) on the data provided in the :doc:`zika tutorial <docs.nextstrain.org:augur/docs/tutorials/zika_tutorial>`, you should see that one of the sequences in the data set was dropped since its name was in the ``dropped_strains.txt`` file.
+If you run this command (you should be able to copy-paste this into your terminal) on the data provided in the :doc:`zika tutorial <docs.nextstrain.org:tutorials/zika_tutorial>`, you should see that one of the sequences in the data set was dropped since its name was in the ``dropped_strains.txt`` file.
 
 Another common filtering operation is subsetting of data to a achieve a more even spatio-temporal distribution or to cut-down data set size to more manageable numbers.
 The filter command allows you to select a specific number of sequences from specific groups, for example one sequence per month from each country: