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/app.py

@@ -173,7 +173,8 @@ def create_app() -> Quart:
 
         from scribe.services.auth import start_auth_token_retention_loop
         from scribe.services.embeddings import (
-            backfill_milestone_embeddings, backfill_note_embeddings, backfill_rule_embeddings,
+            backfill_milestone_embeddings, backfill_note_embeddings,
+            backfill_rule_embeddings, backfill_system_embeddings,
         )
         from scribe.services.logging import start_log_retention_loop
         from scribe.services.notifications import start_notification_loop
@@ -243,6 +244,13 @@ def create_app() -> Quart:
                 await backfill_milestone_embeddings()
             except Exception:
                 logger.warning("Milestone embedding backfill failed", exc_info=True)
+            # Systems got vectors in #4251, so before this pass every charter
+            # ever written is unfindable — a System could narrow a search and
+            # never be the answer to one.
+            try:
+                await backfill_system_embeddings()
+            except Exception:
+                logger.warning("System embedding backfill failed", exc_info=True)
             # Snippets written before migration 0070 have no `notes.data` mirror,
             # and the location reverse lookup queries that column — an unfilled
             # row would read as "no snippet here" rather than as a gap. Separate

src/scribe/mcp/tools/search.py

@@ -15,7 +15,7 @@ from scribe.services.knowledge import content_type_filters
 from scribe.services.text import MATCHED_PASSAGE, excerpt_fields
 from scribe.services.embeddings import (
     DEFAULT_SIMILARITY_THRESHOLD, semantic_search_milestones, semantic_search_notes,
-    semantic_search_rules,
+    semantic_search_rules, semantic_search_systems,
 )
 from scribe.services import rulebooks as rulebooks_svc
 from scribe.services.retrieval_telemetry import record_retrieval, retrieval_summary
@@ -38,7 +38,7 @@ _EXCERPT_CHARS = 1000
 # These two do not reach `semantic_search_notes` at all: they have their own
 # search and their own result shape, so they are dispatched before the mapping
 # and passed in only so the refusal message lists everything THIS door takes.
-_OWN_SEARCH = ("rule", "milestone")
+_OWN_SEARCH = ("rule", "milestone", "system")
 
 
 async def _search_rules(uid: int, q: str, limit: int, project_id: int) -> dict:
@@ -141,6 +141,53 @@ async def _search_milestones(uid: int, q: str, limit: int, project_id: int) -> d
     }
 
 
+async def _search_systems(uid: int, q: str, limit: int, project_id: int) -> dict:
+    """Systems by meaning — "where does this belong?" (#4251).
+
+    A System's `description` is a charter: several hundred words saying what
+    belongs in that area and what does not. `list_systems` enumerates them and
+    `system_id` filters by one, so before this a System could NARROW a search
+    and could never be the answer to one — an agent asking where a record
+    belonged had to read every charter or guess.
+
+    Its own result shape and its own search, not a `content_type` over notes,
+    because the question is different: "where does this belong?" is not "what
+    prior art is there?". A charter competing with the whole note corpus for
+    one top-k would also be outranked by the records filed under it, and the
+    right answer would be crowded out by its own contents.
+
+    The charter's `matched` passage comes along rather than the whole thing.
+    A charter is long and the paragraph that decides where a record belongs is
+    the one worth reading; the rest is get_system (#4243).
+
+    The id that comes back is the one `search(system_id=…)`,
+    `list_system_records` and every `system_ids` argument take — so the answer
+    to "where does this belong?" is directly usable as "show me what is there"
+    and as "file it here".
+    """
+    report: dict = {}
+    raw = await semantic_search_systems(
+        uid, q, project_id=project_id or None, limit=limit, report=report,
+    )
+    chunks = report.get("best_chunk") or {}
+    return {
+        "results": [
+            {
+                "id": sys_.id,
+                "name": sys_.name,
+                **excerpt_fields(
+                    sys_.description or "", chunks.get(int(sys_.id)),
+                    _EXCERPT_CHARS, key="matched",
+                ),
+                "project_id": sys_.project_id,
+                "similarity": float(score),
+            }
+            for score, sys_ in raw
+        ],
+        "total": len(raw),
+    }
+
+
 def result_excerpt(note, chunk: dict | None) -> dict:
     """The part of a record a caller judges "should I open this?" on.
 
@@ -204,8 +251,14 @@ async def search(
             claim that the corpus holds nothing, and a typo must not be able
             to make that claim.
 
-            Or 'rule' (RULES only — the operator's standing
-            instructions, searchable by meaning since milestone 307).
+            THREE KINDS WITH THEIR OWN SEARCH AND THEIR OWN RESULT SHAPE,
+            because each answers a question no note search can:
+            'rule' (the operator's standing instructions — searchable by
+            meaning since milestone 307), 'milestone' ("is there already a
+            plan for this?"), and 'system' ("where does this belong?" — a
+            System's charter says what belongs in an area and what does not,
+            and the id it returns is the one `system_id` and `system_ids`
+            take).
             Reach for 'rule' when you want to know whether a standing
             instruction covers something: "is there a rule about release
             tagging?". A hit carries the rule's `why` and `how_to_apply`,
@@ -258,6 +311,8 @@ async def search(
         return await _search_rules(uid, q, limit, project_id)
     if content_type == "milestone":
         return await _search_milestones(uid, q, limit, project_id)
+    if content_type == "system":
+        return await _search_systems(uid, q, limit, project_id)
     filters = content_type_filters(content_type, extra=_OWN_SEARCH)
     is_task = filters.get("is_task")
     t0 = time.perf_counter()

src/scribe/models/__init__.py

@@ -53,7 +53,9 @@ from scribe.models.user import User  # noqa: E402, F401
 from scribe.models.app_log import AppLog  # noqa: E402, F401
 from scribe.models.password_reset import PasswordResetToken  # noqa: E402, F401
 from scribe.models.invitation import InvitationToken  # noqa: E402, F401
-from scribe.models.embedding import MilestoneEmbedding, NoteEmbedding, RuleEmbedding  # noqa: E402, F401
+from scribe.models.embedding import (  # noqa: E402, F401
+    MilestoneEmbedding, NoteEmbedding, RuleEmbedding, SystemEmbedding,
+)
 from scribe.models.retrieval_log import RetrievalLog  # noqa: E402, F401
 from scribe.models.retrieval_tuning import RetrievalTuningEvent  # noqa: E402, F401
 from scribe.models.note_usage import NoteUsageEvent  # noqa: E402, F401

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),
+    )

src/scribe/services/backup.py

@@ -123,7 +123,7 @@ _BACKED_UP = [
 
 # Tables intentionally NOT in the backup, surfaced in the payload so the gap is
 # explicit rather than silent. ACL (groups/shares) is a coherent follow-up;
-# note_embeddings and rule_embeddings are derived (regenerated at startup
+# the four *_embeddings tables are derived (regenerated at startup
 # from the records themselves, which is also how a chunker bump is handled); api_keys are
 # sensitive credentials; retrieval_logs is observational telemetry that nothing
 # reads for correctness and that grows per query; the rest are
@@ -135,6 +135,7 @@ _BACKED_UP = [
 _NOT_INCLUDED = [
     "groups", "group_memberships", "project_shares", "note_shares",
     "api_keys", "note_embeddings", "rule_embeddings", "milestone_embeddings",
+    "system_embeddings",
     "app_logs", "notifications",
     "invitation_tokens", "password_reset_tokens", "user_profiles",
     "retrieval_logs",

src/scribe/services/embeddings.py

@@ -29,6 +29,7 @@ from scribe.services.access import can_read_project, notes_visibility_clause
 if TYPE_CHECKING:  # resolves forward refs without importing at runtime
     from scribe.models.milestone import Milestone
     from scribe.models.rulebook import Rule
+    from scribe.models.system import System
 
 logger = logging.getLogger(__name__)
 
@@ -1451,6 +1452,211 @@ async def semantic_search_milestones(
     return kept
 
 
+# --- Systems: the charter as an ANSWER, not a filter (#4251) -----------------
+
+
+def system_document(
+    name: str | None, description: str | None
+) -> tuple[str | None, str | None]:
+    """The (title, body) a System is EMBEDDED as — its name and its charter.
+
+    The plainest of the four document shapes, and deliberately so. A System's
+    `description` is already written as the thing this search has to match: it
+    says what belongs in the area and what does not, which is the answer to
+    "where does this go?" in the words someone asking would use. There is no
+    trigger to synthesise, as `rule_document` must, and no separate record to
+    gather in, as `task_document` must — the stored charter IS the sharp
+    document, the way a snippet's is.
+
+    `color`, `status` and `order_index` are left out. They are presentation and
+    bookkeeping; a vector that carried them would be answering a question
+    nobody asks of a charter.
+
+    A System with no charter yet degrades to its name. It still embeds, just
+    weakly — a bare name is exactly what the model docstring says is never
+    enough, and this is an argument for writing the charter, not for padding
+    the document with whatever is to hand.
+    """
+    return (name or "").strip() or None, (description or "").strip() or None
+
+
+async def upsert_system_embedding(
+    system_id: int, name: str | None, description: str | None
+) -> None:
+    """Chunk, embed and persist a System's vectors. Safe to fire-and-forget.
+
+    The third sibling's contract exactly: one document definition shared by the
+    write path and the backfill, and an atomic per-System replacement guarded
+    by the parent-row claim (#3262), so a System deleted mid-refresh wins.
+    """
+    from scribe.models.embedding import SystemEmbedding
+    from scribe.models.system import System
+
+    doc_title, doc_body = system_document(name, description)
+    chunks = chunk_document(doc_title, doc_body)
+    try:
+        if not chunks:
+            async with async_session() as session:
+                await session.execute(
+                    delete(SystemEmbedding).where(SystemEmbedding.system_id == system_id)
+                )
+                await session.commit()
+            return
+    except Exception:
+        logger.warning("Failed to clear embedding for system %d", system_id, exc_info=True)
+        return
+
+    try:
+        vectors = await get_embeddings(chunks)
+    except Exception:
+        logger.debug("Skipping embedding for system %d — embedder unavailable", system_id)
+        return
+
+    try:
+        async with async_session() as session:
+            if not await _claim_parent_row(session, System.id, system_id, "system"):
+                return
+            await session.execute(
+                delete(SystemEmbedding).where(SystemEmbedding.system_id == system_id)
+            )
+            for index, (chunk, vector) in enumerate(zip(chunks, vectors)):
+                session.add(SystemEmbedding(
+                    system_id=system_id, chunk_index=index, embedding=vector,
+                    chunk_text=chunk, chunker_version=CHUNKER_VERSION,
+                ))
+            await session.commit()
+    except Exception:
+        logger.warning("Failed to persist embedding for system %d", system_id, exc_info=True)
+
+
+async def semantic_search_systems(
+    user_id: int,
+    query: str,
+    *,
+    project_id: int | None = None,
+    limit: int = 5,
+    threshold: float = _SIMILARITY_THRESHOLD,
+    report: dict | None = None,
+) -> list[tuple[float, "System"]]:
+    """Return up to *limit* (score, system) pairs most like *query*.
+
+    Answers "where does this belong?" — the question asked before filing a
+    record or opening a file, and the one that had no tool: `list_systems`
+    enumerates and `system_id` filters, so a charter could narrow a search and
+    could never be the answer to one.
+
+    ITS OWN SEARCH rather than a note kind, for what note 3163 says about
+    milestones: a charter competing with the whole note corpus for one top-k
+    would be outranked by the records filed under it, and the right answer
+    would be crowded out by its own contents. The questions are different too —
+    "where does this belong?" is not "what prior art is there?" — and a caller
+    asking one should not have to read past answers to the other.
+
+    SCOPE. With `project_id`, that project's Systems, provided the caller can
+    read the project (access.can_read_project, rule 78) — a collaborator on a
+    shared project sees its areas, which is the point of a charter. Without
+    one, the Systems the caller owns across their projects. Archived Systems
+    are excluded: an archived area is one the operator has said is no longer
+    where things go, and that is exactly the question being asked.
+
+    Collapses to best-chunk-per-System and publishes the winning chunk, like
+    the sibling searches — from the start rather than retrofitted (#4243).
+    Returns an empty list if the embedder is unavailable, the project is not
+    readable, or on any error: a recall aid must never break the call it
+    serves.
+    """
+    from scribe.models.embedding import SystemEmbedding
+    from scribe.models.system import System
+
+    if not query or not query.strip():
+        return []
+    try:
+        query_vec = await get_embedding(query)
+    except Exception:
+        logger.debug("System search skipped — embedder unavailable")
+        return []
+
+    distance = SystemEmbedding.embedding.cosine_distance(query_vec)
+    try:
+        if project_id:
+            if not await can_read_project(user_id, project_id):
+                return []
+            scope = System.project_id == project_id
+        else:
+            scope = System.user_id == user_id
+        async with async_session() as session:
+            rows = (await session.execute(
+                select(
+                    System,
+                    distance.label("distance"),
+                    SystemEmbedding.chunk_index,
+                    SystemEmbedding.chunk_text,
+                )
+                .select_from(SystemEmbedding)
+                .join(System, SystemEmbedding.system_id == System.id)
+                .where(
+                    scope,
+                    System.deleted_at.is_(None),
+                    System.status != "archived",
+                )
+                .order_by(distance)
+                .limit(limit * _CHUNK_OVERFETCH)
+            )).all()
+    except Exception:
+        logger.warning("System semantic search failed", exc_info=True)
+        return []
+
+    best: dict[int, tuple[float, object]] = {}
+    # A charter runs to several hundred words and a result shows its NAME — so
+    # a match on the paragraph that actually decides where a record belongs
+    # would be previewed by two words that cannot. The winning chunk is what
+    # the caller should see (#4243).
+    won: dict[int, dict] = {}
+    for system, dist, chunk_index, chunk_text in rows:
+        score = 1.0 - float(dist)
+        if system.id not in best or score > best[system.id][0]:
+            best[system.id] = (score, system)
+            won[int(system.id)] = {
+                "index": int(chunk_index), "text": chunk_text or "",
+            }
+    ranked = sorted(best.values(), key=lambda pair: pair[0], reverse=True)
+    kept = [pair for pair in ranked if pair[0] >= threshold][:limit]
+    record_best_chunk(report, {
+        int(sys_.id): won[int(sys_.id)] for _s, sys_ in kept if int(sys_.id) in won
+    })
+    return kept
+
+
+async def backfill_system_embeddings() -> None:
+    """Embed Systems that have no current vectors. Runs at startup beside the
+    note, rule and milestone backfills; a CHUNKER_VERSION bump re-embeds.
+
+    This is also the pass that makes every existing charter findable at all —
+    Systems got vectors in #4251, so before it runs there are none."""
+    from scribe.models.embedding import SystemEmbedding
+    from scribe.models.system import System
+
+    try:
+        async with async_session() as session:
+            current = select(SystemEmbedding.system_id).where(
+                SystemEmbedding.chunker_version == CHUNKER_VERSION
+            )
+            stale = (await session.execute(
+                select(System.id, System.name, System.description)
+                .where(System.deleted_at.is_(None), System.id.notin_(current))
+            )).all()
+    except Exception:
+        logger.warning("System embedding backfill: failed to query systems", exc_info=True)
+        return
+
+    if not stale:
+        logger.info("System embedding backfill: all systems current at chunker v%d", CHUNKER_VERSION)
+        return
+    logger.info("System embedding backfill: embedding %d system(s)", len(stale))
+    for system_id, name, description in stale:
+        await upsert_system_embedding(system_id, name, description)
+
+
 async def backfill_milestone_embeddings() -> None:
     """Embed milestones that have no current vectors. Runs at startup beside
     the note and rule backfills; a CHUNKER_VERSION bump re-embeds."""

src/scribe/services/systems.py

@@ -114,6 +114,38 @@ async def seed_standard_systems(user_id: int, project_id: int) -> list[System]:
     return out
 
 
+def embed_system(system) -> None:
+    """Refresh a System's charter vectors, fire-and-forget (#4251).
+
+    The twin of `notes.embed_note`, and here for the same reason (#2056): at
+    the service, so every door gets it by construction rather than each route
+    and tool remembering. A charter edited through one door and not another
+    would stay findable by what it used to say, and nothing would report it.
+
+    Not called on delete. `delete_system` is a SOFT delete and the search joins
+    through `System`, so a deleted System's vectors are already unreachable —
+    and leaving them means a restore is findable again immediately instead of
+    waiting for the next startup backfill.
+
+    Import is lazy so importing this module doesn't pull in the embedding
+    model; a missing event loop (unit tests, scripts) is ordinary, not an
+    error; exceptions are swallowed because a System that saved must not fail
+    on its index refresh.
+    """
+    try:
+        import asyncio
+
+        from scribe.services.embeddings import upsert_system_embedding
+
+        asyncio.create_task(
+            upsert_system_embedding(system.id, system.name, system.description)
+        )
+    except RuntimeError:
+        pass          # no running loop — a sync caller, not a failure
+    except Exception:  # noqa: BLE001 - never let indexing break a write
+        logger.exception("embedding refresh failed for system %s", system.id)
+
+
 async def create_system(
     user_id: int,
     project_id: int,
@@ -144,6 +176,7 @@ async def create_system(
         session.add(system)
         await session.commit()
         await session.refresh(system)
+        embed_system(system)
         return system
 
 
@@ -195,6 +228,7 @@ async def update_system(user_id: int, system_id: int, **fields: object) -> Syste
         system.updated_at = datetime.now(timezone.utc)
         await session.commit()
         await session.refresh(system)
+        embed_system(system)
         return system