fix: ignore deleted paths in generated entities

closes #806

Author: rokroskar

renku/core/models/provenance/activities.py

@@ -192,6 +192,11 @@ def paths(self):
         index = set()
 
         for file_ in self.commit.diff(self.commit.parents or NULL_TREE):
+            # ignore deleted files (note they appear as ADDED)
+            # in this backwards diff
+            # TODO: set `deprecatedBy` for deleted paths
+            if file_.change_type == 'A':
+                continue
             path_ = Path(file_.a_path)
 
             is_dataset = self.client.DATASETS in str(path_)