move common code into server, update tests and makefile (#2425)

* move common code into server, update tests and makefile

remove backend directory, refactor

update smoke tests

test/unit/cli/test_prepare.py

@@ -0,0 +1,15 @@
+import unittest
+
+import pandas as pd
+
+from server.cli.prepare import make_index_unique
+
+
+class CLIPrepareTests(unittest.TestCase):
+    """ Test cases for CLI prepare logic """
+
+    def test_make_index_unique(self):
+        index = pd.Index(["SNORD113", "SNORD113", "SNORD113-1"])
+        result = make_index_unique(index)
+        expected = pd.Index(["SNORD113", "SNORD113-2", "SNORD113-1"])
+        self.assertTrue(all(left == right for left, right in zip(result.values, expected.values)))