docs(6209): preference door, systems and notes tools, lesson surfacing, rule versions, backup round trip, JSON reader, charter search, provenance, location filter

Ten more test files: issue, milestone, rule, decision and snippet numbers
come out of docstrings, comments and messages; the preference door states
what a preference is instead of quoting the framing; the JSON reader says
why jq is not assumed instead of what every hook used to do; the backup
round trip's column warning no longer claims the import side is unguarded.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

tests/test_mcp_tool_notes.py

@@ -15,10 +15,10 @@ pytestmark = pytest.mark.usefixtures("_bind_user")
 
 @pytest.fixture(autouse=True)
 def _no_supersession():
-    """Every note read/write now asks for its supersession relations (#278).
+    """Every note read/write asks for its supersession relations.
 
     These are unit tests of the TOOL layer and this job has no database — the
-    same hazard the `_fake_note` comment below records for note 2109. Stubbed
+    same hazard the `_fake_note` comment below records. Stubbed
     to "no relations", which is the state of essentially every note; the
     relation's own behaviour is covered in test_services_supersession.py, and
     the attachment is covered explicitly below.
@@ -120,7 +120,7 @@ async def test_get_note_returns_dict():
     # Own record: no provenance noise.
     assert "shared" not in out
     # No supersession relations: both keys ABSENT, not present-and-empty. A
-    # field that always says nothing trains readers to skip fields (#2483).
+    # field that always says nothing trains readers to skip fields.
     assert "supersedes" not in out
     assert "superseded_by" not in out
 
@@ -218,7 +218,7 @@ async def test_update_note_only_sends_non_default_fields():
 
     `clear` is always forwarded and is not a field: it is how this door says
     "unset these", and an empty one says "unset nothing". Same shape the rules
-    door took in #3096, and the same test that had to learn about it there."""
+    door takes, and the same test."""
     fake = fake_note()
     mock = AsyncMock(return_value=fake)
     with patch("scribe.mcp.tools.notes.notes_svc.update_note", mock):
@@ -232,7 +232,7 @@ async def test_update_note_only_sends_non_default_fields():
 @pytest.mark.asyncio
 async def test_update_note_forwards_a_check_but_not_an_empty_one():
     """"" means "leave this alone" at this door — an agent updating a body must
-    not wipe a check it was never asked about (milestone 317)."""
+    not wipe a check it was never asked about."""
     mock = AsyncMock(return_value=fake_note())
     with patch("scribe.mcp.tools.notes.notes_svc.update_note", mock):
         await update_note(note_id=1, verify_with="curl the docs")
@@ -305,7 +305,7 @@ async def test_delete_note_soft_deletes_and_returns_batch():
     ):
         result = await delete_note(note_id=7)
     assert result["deleted_batch_id"] == "batch-1"
-    # The confirmation NAMES what went (#3273). After the delete the row is
+    # The confirmation NAMES what went. After the delete the row is
     # trashed, so this line is the last chance to say which note it was.
     assert result["title"] == "the note that went"
     assert "the note that went" in result["message"]