Keep runtime evidence exclusion scoped to the repository root

Co-Authored-By: Paperclip <noreply@paperclip.ing>

server/src/__tests__/cli-invocation-safety.test.ts

@@ -335,8 +335,6 @@ const SKIP_DIRS = new Set([
   ".next",
   "coverage",
   ".paperclip",
-  // Ignored local databases and downloaded acceptance evidence are not guidance.
-  ".paperclip-runtime",
   "tmp",
 ]);