Fix warnings in project.json

PR #2493 introduced the new project.json schema. The tree has 118 files
with the old schema, which added several hundred warnings.

This change can't go in until PR #2864 does - it relies on those bug
fixes.

TestAssets/TestPackages/PackageWithFakeNativeDep/project.json

@@ -1,9 +1,13 @@
 {
   "version": "1.0.0",
-  "packInclude": {
-      "runtimes/": "runtimes/"
-  },
   "frameworks": {
-      "net45": {}
+    "net45": {}
+  },
+  "packOptions": {
+    "files": {
+      "mappings": {
+        "runtimes/": "runtimes/"
+      }
+    }
   }
 }