From f2ade9d92ec7f51e4eac9509922dff47cd272c50 Mon Sep 17 00:00:00 2001
From: Joe Danziger <joe@ticc.net>
Date: Mon, 5 Oct 2026 15:17:15 -0400
Subject: [PATCH] doctor: resolve duplicate stems in the indexer's order

Two doctor checks built their stem map from component-sorted paths while the
indexer (and relink) use plain string order, so a bare [[Dup]] could resolve
to a different note in cross-refs and near-duplicate checks than in search.

Claude-Session: https://claude.ai/code/session_012XGaE1cGxpYryus7cxfAFD
---
 src/brain/doctor.py  |  4 ++--
 tests/test_doctor.py | 17 +++++++++++++++++
 2 files changed, 19 insertions(+), 2 deletions(-)

diff --git a/src/brain/doctor.py b/src/brain/doctor.py
index 054c22c..d90af49 100644
--- a/src/brain/doctor.py
+++ b/src/brain/doctor.py
@@ -436,7 +436,7 @@ def _check_duplicates(master: Path, org: Org, rules: tuple[SpaceRule, ...],
     # siblings under one parent still are.
     all_paths = set(rels)
     by_stem_all: dict[str, str] = {}
-    for r in rels:
+    for r in sorted(rels):  # string order, as the indexer resolves duplicate stems
         by_stem_all.setdefault(_stem(r), r)
     up_of: dict[str, set[str]] = {}
     for r in rels:
@@ -831,7 +831,7 @@ def _check_cross_space_refs(master: Path, org: Org, rules: tuple[SpaceRule, ...]
     rels = run.content_files()
     paths = set(rels)
     by_stem: dict[str, str] = {}
-    for rel in rels:
+    for rel in sorted(rels):  # string order, as the indexer resolves duplicate stems
         by_stem.setdefault(_stem(rel), rel)
 
     readers_of = run.readers_of(org, rules)
diff --git a/tests/test_doctor.py b/tests/test_doctor.py
index e7f423b..4ec3004 100644
--- a/tests/test_doctor.py
+++ b/tests/test_doctor.py
@@ -123,6 +123,23 @@ def test_cross_space_reference_warns_and_same_space_is_silent(master):
     assert "bob" in home[0].message           # the reader who cannot see it
 
 
+def test_cross_refs_resolve_duplicate_stems_like_the_indexer(master):
+    seed_meta(master)
+    # "Clients/a-b/Dup.md" sorts before "Clients/a/Dup.md" as a string ('-' < '/'),
+    # which is the order the indexer resolves a bare [[Dup]] in. Doctor must pick
+    # the same note: the public one, so the link leaks nothing.
+    (master / "_meta/spaces.yaml").write_text(
+        SPACES_YAML
+        + '  - {path: "Clients/a", read: ["person:alice"], write: ["person:alice"]}\n'
+        + '  - {path: "Clients/a-b", read: [everyone], write: ["person:alice"]}\n')
+    for rel in ("Clients/a/Dup.md", "Clients/a-b/Dup.md"):
+        (master / rel).parent.mkdir(parents=True, exist_ok=True)
+        (master / rel).write_text("# Dup\nbody.\n")
+    (master / "Company/Pointer.md").write_text("# Pointer\nSee [[Dup]].\n")
+    findings = [f for f in run_doctor(master) if f.check == "cross-refs"]
+    assert not [f for f in findings if f.message.startswith("Company/Pointer.md")]
+
+
 def _restrict_vandenberg(master):
     """Add a Vandenberg client space readable only by alice."""
     (master / "_meta/spaces.yaml").write_text(