Diff refine JSONs with custom script in functional tests

Updates functional tests to use the diff_jsons.py script instead of the
vanilla UNIX diff. This script allows tests to ignore changes in output
like the augur version number that should not be considered in diffs
anyway. This fix is required for the next augur release.

tests/functional/refine.t

@@ -69,7 +69,8 @@ Confirm that trees match expected topology and branch lengths, given that the ou
 
   $ python3 "$TESTDIR/../../scripts/diff_trees.py" "refine/not_time_tree.nwk" "$TMP/tree.nwk" --significant-digits 2
   {}
-  $ diff -u "refine/mutations_per_site_branch_lengths.json" "$TMP/branch_lengths.json"
+  $ python3 "$TESTDIR/../../scripts/diff_jsons.py" "refine/mutations_per_site_branch_lengths.json" "$TMP/branch_lengths.json" --significant-digits 0
+  {}
 
 Run refine again without a time tree, but request number of mutations per branch as the divergence unit.
 This approach only works when we provide an alignment FASTA.
@@ -93,7 +94,8 @@ Confirm that trees match expected topology and branch lengths, given that the ou
 
   $ python3 "$TESTDIR/../../scripts/diff_trees.py" "refine/not_time_tree.nwk" "$TMP/tree.nwk" --significant-digits 2
   {}
-  $ diff -u "refine/integer_branch_lengths.json" "$TMP/branch_lengths.json"
+  $ python3 "$TESTDIR/../../scripts/diff_jsons.py" "refine/integer_branch_lengths.json" "$TMP/branch_lengths.json" --significant-digits 0
+  {}
 
 Run refine again without a time tree, but try to request number of mutations per branch as the divergence unit.
 This approach does not make sense and should not work without an alignment FASTA.