Update docs to reflect removal of export v1

Includes updating & adding the redirects so that v1 URLs go to the
(v1→v2) migration guide as well as removal of all relevant references
to "augur export v1"

Author: jameshadfield

Diff for: docs/api/developer/augur.export_v1.rst

@@ -35,7 +35,6 @@ Submodules
    augur.distance
    augur.errors
    augur.export
-   augur.export_v1
    augur.export_v2
    augur.frequencies
    augur.frequency_estimators

Diff for: docs/api/developer/augur.rst

@@ -2,7 +2,7 @@
 
 Auspice uses a number of default color schemes to color the tree using meta data or values that the augur pipeline computed. In some cases these defaults are not suitable for particular type of data, and you'd like to use your own color schemes.
 
-To specify a mapping between discrete trait values and colors, you can pass a tab-delimited file to `augur export`/`augur export v1`/`augur export v2` using `--colors`.
+To specify a mapping between discrete trait values and colors, you can pass a tab-delimited file to `augur export v2` using `--colors`.
 
 > _Note that it's not currently possible to specify color schemes for nucleotides, amino acids, or continuous data._
 

Diff for: docs/faq/colors.md

@@ -55,9 +55,9 @@ posterior           273         0
 ```
 augur import beast --mcc data/MERS_CoV_mcc.tree --output-tree results/mers.new
     --output-node-data results/beast_data.json
-augur export v1 --tree results/mers.new --node-data results/beast_data.json
+augur export v2 --tree results/mers.new --node-data results/beast_data.json
     --auspice-config config/auspice_config.json
-    --output-tree auspice/mers_tree.json --output-meta auspice/mers_meta.json
+    --output auspice/mers.json
 ```
 
 ```

Diff for: docs/faq/import-beast.md

@@ -72,16 +72,13 @@ Consistancy and Style
 ~~~~~~~~~~~~~~~~~~~~~
 
 Check that your metadata is free from spelling mistakes and that values
-are consistant. Augur doesn't know that 'UK' and 'United Kingdom' or
+are consistent. Augur doesn't know that 'UK' and 'United Kingdom' or
 'cat' and 'feline' are the same!
 
-Previously, auspice 'prettified' traits by capitalizing them
+Note: Previously, auspice 'prettified' traits by capitalizing them
 automatically, and removing the underscores that separated two-word
-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`` (:ref:`read more <prettifying-metadata-fields>`).
+locations ('new_zealand' became 'New Zealand'). With `augur export v2`
+this is no longer the case, see :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

Diff for: docs/faq/metadata.rst

@@ -82,7 +82,11 @@
 
 - type: page
   from_url: /api/augur.export_v1.html
-  to_url: /api/developer/augur.export_v1.html
+  to_url: /releases/migrating-v5-v6.html
+
+- type: page
+  from_url: /api/developer/augur.export_v1.html
+  to_url: /releases/migrating-v5-v6.html
 
 - type: page
   from_url: /api/augur.export_v2.html