feat(retrieval): a System's charter becomes an answer, not just a filter (#4251)

Step 2 of #4251. A System's `description` is a charter — several hundred words
saying what belongs in that area and what does not — and it is the answer to
"which part of this codebase does X live in". There was no semantic path to
one: `list_systems` enumerates, and `search(system_id=…)` uses a System as a
FILTER over notes. So a System could narrow a search and could never be the
answer to one, and an agent asking where a record belonged had to read every
charter or guess.

ITS OWN SEARCH, not a `content_type` over notes, for the reason note 3163
gives about milestones: the row could be shared, the search cannot. A charter
competing with the whole note corpus for one top-k is outranked by the records
filed under it — the right answer crowded out by its own contents — and "where
does this belong?" is a different question from "what prior art is there?",
which a caller asking one should not have to read past answers to.

So `system_embeddings` (0107) joins note_, rule_ and milestone_embeddings as
the fourth sibling, with `system_document`, `upsert_system_embedding`,
`semantic_search_systems`, a startup backfill and `search(content_type=
"system")`. Scoped like milestones: with a project_id, that project's Systems
if the caller can read the project (rule 78); without one, the caller's own.
Archived Systems are excluded — an archived area is one the operator has said
is no longer where things go, which is exactly the question being asked.

`system_document` is the plainest of the four shapes on purpose. A charter is
already written as the thing this search has to match, in the words someone
asking would use — so there is no trigger to synthesise as `rule_document`
must, and no second record to gather as `task_document` must. The stored
charter IS the sharp document, the way a snippet's is. `color`, `status` and
`order_index` stay out: presentation and bookkeeping, and a vector carrying
them would be answering a question nobody asks of a charter.

The search publishes `report["best_chunk"]` from the start rather than being
retrofitted, which is what #4251 asked of any fourth search. It matters more
here than anywhere: a charter runs long and a result shows its NAME, so a match
on the paragraph that actually decides where a record belongs would otherwise
be previewed by two words that cannot say.

The id that comes back is the one `system_id`, `system_ids` and
`list_system_records` already take, so the answer to "where does this belong?"
is directly usable as "show me what is there" and as "file it here".

`embed_system` sits beside `notes.embed_note` at the service for #2056's
reason — every door gets it by construction. Not called on delete: that is a
soft delete and the search joins through `System`, so the vectors are already
unreachable, and leaving them means a restore is findable again immediately.
`system_embeddings` is declared in backup's `_NOT_INCLUDED` as derived, beside
its three siblings.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01821k5B3Ysecp9fNYs92Kuy

src/scribe/models/embedding.py

@@ -128,3 +128,42 @@ class MilestoneEmbedding(Base):
         DateTime(timezone=True),
         default=lambda: datetime.now(timezone.utc),
     )
+
+
+class SystemEmbedding(Base):
+    """One embedding vector per CHUNK of a System's charter (#4251).
+
+    The fourth sibling, for the reason note 3163 gives about the third: the row
+    could be shared, the search cannot. A System's `description` is a charter —
+    several hundred words saying what belongs in that area and what does not —
+    and it is the answer to "which part of this codebase does X live in".
+    Before this there was no semantic path to one: `list_systems` enumerates,
+    and `search(system_id=…)` uses a System as a FILTER over notes. So a System
+    could narrow a search and could never be the answer to one.
+
+    "Where does this belong?" is a different question from "what prior art is
+    there?", which is why this is its own search rather than a note_type: a
+    charter competing with two thousand notes for the same top-k would be
+    outranked by the records filed under it, and the right answer would be
+    crowded out by its own contents.
+
+    The document is the name and the charter. Derived data: the startup
+    backfill regenerates it, which is also how a chunker-version bump is
+    handled.
+    """
+
+    __tablename__ = "system_embeddings"
+
+    system_id: Mapped[int] = mapped_column(
+        Integer,
+        ForeignKey("systems.id", ondelete="CASCADE"),
+        primary_key=True,
+    )
+    chunk_index: Mapped[int] = mapped_column(Integer, primary_key=True)
+    embedding: Mapped[list] = mapped_column(Vector(EMBEDDING_DIM), nullable=False)
+    chunk_text: Mapped[str] = mapped_column(Text, nullable=False)
+    chunker_version: Mapped[int] = mapped_column(Integer, nullable=False)
+    updated_at: Mapped[datetime] = mapped_column(
+        DateTime(timezone=True),
+        default=lambda: datetime.now(timezone.utc),
+    )