remove augur refine and skip validation

tests/functional/export_v2/cram/minify-output.t

@@ -11,34 +11,33 @@ names to create larger file sizes with less recursion.
   >   if [ $n -eq 1 ]; then
   >        echo "$prefix$n"
   >    else
-  >        echo "($(generate_newick $((n-1))),$prefix$n)"
+  >        echo "($prefix$n,$(generate_newick $((n-1)))):INTERNAL_$n"
   >    fi
   > }
 
 A small tree is not automatically minified.
-The unminified output is 15KB which is considered acceptable.
+The unminified output is 13KB which is considered acceptable.
 
-  $ echo "$(generate_newick 10);" > small_tree_raw.nwk
-
-Use augur refine to add internal node names
-  $ ${AUGUR} refine --tree small_tree_raw.nwk --output-tree small_tree.nwk  &>/dev/null
+  $ echo "$(generate_newick 10);" > small_tree.nwk
 
 
   $ ${AUGUR} export v2 \
   >   --tree small_tree.nwk \
+  >   --skip-validation \
   >   --output output.json &>/dev/null
 
   $ head -c 20 output.json
   {
     "version": "v2", (no-eol)
 
   $ ls -l output.json | awk '{print $5}'
-  15039
+  13886
 
 It can be forcefully minified with an argument.
 
   $ ${AUGUR} export v2 \
   >   --tree small_tree.nwk \
+  >   --skip-validation \
   >   --minify-json \
   >   --output output.json &>/dev/null
 
@@ -50,22 +49,21 @@ even if it may seem "falsey".
 
   $ AUGUR_MINIFY_JSON=0 ${AUGUR} export v2 \
   >   --tree small_tree.nwk \
+  >   --skip-validation \
   >   --output output.json &>/dev/null
 
   $ head -c 20 output.json
   {"version": "v2", "m (no-eol)
 
 
-A large tree, when forcefully not minified, has an output size of 8MB which is
+A large tree, when forcefully not minified, has an output size of 6MB which is
 considered large.
 
-  $ echo "$(generate_newick 500);" > big_tree_raw.nwk
-
-Use augur refine to add internal node names
-  $ ${AUGUR} refine --tree big_tree_raw.nwk --output-tree big_tree.nwk  &>/dev/null
+  $ echo "$(generate_newick 500);" > big_tree.nwk
 
   $ ${AUGUR} export v2 \
   >   --tree big_tree.nwk \
+  >   --skip-validation \
   >   --no-minify-json \
   >   --output output.json &>/dev/null
 
@@ -74,7 +72,7 @@ Use augur refine to add internal node names
     "version": "v2", (no-eol)
 
   $ ls -l output.json | awk '{print $5}'
-  8591420
+  6573338
 
 This means it is automatically minified.
 
@@ -87,4 +85,4 @@ This means it is automatically minified.
   {"version": "v2", "m (no-eol)
 
   $ ls -l output.json | awk '{print $5}'
-  576414
+  566320