harness v1.3: create repo/ symlink inside run_tests (after clean_state)

scripts/verify.py

@@ -1,4 +1,4 @@
-"""PatchBench row verification + context expansion harness (v1.2).
+"""PatchBench row verification + context expansion harness (v1.3).
 
 For each candidate row:
   1. clone the repo at base_commit
@@ -41,6 +41,11 @@ repo/Cargo.toml) from the upstream /testbed/repo convention -- a self-symlink no
 makes both layouts resolve. Context expansion skips test files referenced by the
 test_patch that don't exist on disk instead of crashing the row (eza 0070).
 
+v1.3: the v1.2 repo-layout symlink was created in verify_row BEFORE clean_state, and
+clean_state runs git clean -fdxq which deleted it -- noir rows ran with no repo/
+self-link and parsed 0 tests. The symlink is now created inside run_tests, after
+every clean_state, so both layouts resolve in every phase.
+
 Usage (inside a job with the right language toolchain image):
   python verify.py --lang go --file pilot/candidates/go.jsonl --limit 6
 """
@@ -238,6 +243,14 @@ def run_tests(row, repo_dir, lang, phase_tag=""):
     """Run rebuild_cmds, test_cmds, print_cmds, then collect the report files the
     test frameworks wrote (surefire/gradle XML, gradle HTML, reports/*) and feed
     them to the log parser. Returns (tests_dict, combined_output_tail)."""
+    # v1.3: rows whose cmds reference a nested repo/ layout need a self-symlink,
+    # and it must exist AFTER every clean_state (which git-cleans it away).
+    _cmds = (row.get("test_cmds") or []) + (row.get("rebuild_cmds") or []) + (row.get("print_cmds") or [])
+    if any(("repo/" in c) or c.rstrip().endswith("/repo") for c in _cmds):
+        _sl = os.path.join(repo_dir, "repo")
+        if not (os.path.islink(_sl) or os.path.exists(_sl)):
+            os.symlink(repo_dir, _sl)
+            print("repo-layout symlink created", flush=True)
     disk_guard(f"{phase_tag}-pre")
     parser = get_parser(row)
     dep_err = ensure_js_deps(repo_dir)
@@ -343,16 +356,6 @@ def verify_row(row, lang):
             return rec
     log_disk(f"cloned:{row['id']}")
 
-    # v1.2: some rows reference a nested repo/ layout (e.g. test_cmds using
-    # "cd repo" or paths ending in /repo) that our flat clone does not have.
-    # Create a self-symlink so both layouts resolve; idempotent on reruns.
-    _cmds = (row.get("test_cmds") or []) + (row.get("rebuild_cmds") or []) + (row.get("print_cmds") or [])
-    if any(("repo/" in c) or c.rstrip().endswith("/repo") for c in _cmds):
-        _sl = os.path.join(repo_dir, "repo")
-        if not (os.path.islink(_sl) or os.path.exists(_sl)):
-            os.symlink(repo_dir, _sl)
-            print("repo-layout symlink created")
-
     if lang == "rust":
         os.environ["CARGO_TARGET_DIR"] = RUST_SHARED_TARGET
         # v1.1: a dev-profile build with debuginfo hit 43G on the 50G container