fix(corpus): advisory-pair repo-overlap -- remove real pilot leaks, skip vendored trees

test_no_pair_repeats_a_repository_the_benchmarks_already_name failed: advisory-fix
catalog repos also appeared elsewhere under benchmarks/. Root cause split two ways:

1. Genuine leak: 16 catalog repos are also subjects in benchmarks/search/private/
   pilot.json (a real private pilot population). Removed those 16 pairs from the
   three catalogs and their verification.json rows (totals recomputed, catalog ==
   verification preserved).
2. Spurious: the overlap scan greped ~49k vendored files under
   benchmarks/search/private/runs/*/checkout/node_modules/, so any catalog repo a
   vendored dependency's README names collided. Added a narrow vendored-tree skip
   (node_modules/vendor) to the scan rather than deleting labelled pairs over a
   dependency mention.

Implemented from Codex's first pass (gpt-6.1-sol), then gated and corrected: Codex
removed 20 pairs; 4 of those (backstage/backstage, koajs/koa, beaugunderson/
ip-address, cakephp/cakephp) were driven only by vendored/non-population mentions
and are kept. Also excluded advisory-fixes-spread.json (catalog-derived report)
and research-2026-09-26.md (selection write-up) as non-population.

tests/test_advisory_fix_pairs.py + tests/test_learn_labels.py: 53 passed.

Co-Authored-By: Claude Opus 4.8 <[email protected]>

benchmarks/pairs/advisory-fixes-2/verification.json

@@ -200,11 +200,6 @@
       "ok": true,
       "bytes_read": 2607
     },
-    {
-      "name": "typeorm-handler-41d1c62",
-      "ok": true,
-      "bytes_read": 11977
-    },
     {
       "name": "velocity-js-isblockedpathkey-f8e47a6",
       "ok": true,
@@ -220,11 +215,6 @@
       "ok": true,
       "bytes_read": 6805
     },
-    {
-      "name": "gitpython-option-candidates-96a888f",
-      "ok": true,
-      "bytes_read": 3421
-    },
     {
       "name": "mermaid-addnamespace-12d472c",
       "ok": true,
@@ -350,11 +340,6 @@
       "ok": true,
       "bytes_read": 5302
     },
-    {
-      "name": "notebooklm-mcp-makeslug-13828d9",
-      "ok": true,
-      "bytes_read": 2103
-    },
     {
       "name": "langchain-nvidia-url-to-b64-string-b483c7c",
       "ok": true,
@@ -415,11 +400,6 @@
       "ok": true,
       "bytes_read": 2750
     },
-    {
-      "name": "axios-setproxy-fb3befb",
-      "ok": true,
-      "bytes_read": 4403
-    },
     {
       "name": "rembg-s-command-07ad0d4",
       "ok": true,
@@ -491,6 +471,6 @@
       "bytes_read": 3385
     }
   ],
-  "verified": 98,
-  "bytes_read": 526134
+  "verified": 94,
+  "bytes_read": 504230
 }