feat: Complete test suite alignment with soft delete

- Update tests to expect soft delete by default behavior
- Add documentation (CHANGELOG.md, MIGRATION.md)
- Fix statistics tests to handle existing data
- Verify both soft and hard delete work correctly
- 12/15 storage tests now passing (2 statistics issues remain)

brainy-data/_system/statistics.json

@@ -0,0 +1,18 @@
+{
+  "nounCount": {
+    "default": 0
+  },
+  "verbCount": {},
+  "metadataCount": {
+    "default": 0
+  },
+  "hnswIndexSize": 1,
+  "lastUpdated": "2025-08-19T01:13:31.471Z",
+  "serviceActivity": {
+    "default": {
+      "firstActivity": "2025-08-19T01:13:26.462Z",
+      "lastActivity": "2025-08-19T01:13:26.467Z",
+      "totalOperations": 4
+    }
+  }
+}

brainy-data/metadata/__metadata_index__deletedAt_2025-08-19t01_chunk0.json

@@ -0,0 +1 @@
+null

brainy-data/metadata/__metadata_index__deletedBy_user_chunk0.json

@@ -0,0 +1 @@
+null

brainy-data/metadata/__metadata_index__deleted___true___chunk0.json

@@ -0,0 +1 @@
+null

brainy-data/metadata/d5478378-9e6c-4c8f-b642-1f2358b0d082.json

@@ -0,0 +1 @@
+null