Reapply changes to newly created files

Author: corneliusroemer

tests/functional/tree/cram/iqtree-extend-args.t

@@ -7,5 +7,5 @@ Build a tree, augmenting existing default arguments with custom arguments.
   $ ${AUGUR} tree \
   >  --method iqtree \
   >  --alignment "$TESTDIR/../data/aligned.fasta" \
-  >  --tree-builder-args="-czb" \
+  >  --tree-builder-args="--polytomy" \
   >  --output tree_raw.nwk > /dev/null

tests/functional/tree/cram/iqtree-override-args.t

@@ -8,6 +8,6 @@ Since the following custom arguments are incompatible with the default IQ-TREE a
   $ ${AUGUR} tree \
   >  --method iqtree \
   >  --alignment "$TESTDIR/../data/full_aligned.fasta" \
-  >  --tree-builder-args="-czb -bb 1000 -bnni" \
+  >  --tree-builder-args="--polytomy -bb 1000 -bnni" \
   >  --override-default-args \
   >  --output tree_raw.nwk > /dev/null