feat(issues): S2 MCP tools — system CRUD + issue/system wiring

Second slice of Issues + Systems (spec #825).

New mcp/tools/systems.py: create_system, list_systems, get_system (records
split into issues/tasks/notes), update_system (incl. archive via status),
list_system_records (kind/open_only filters), delete_system. Registered in
register_all; read tools (get_system, list_systems, list_system_records) added
to the read-only-key allowlist (write tools default-deny).

create_task/update_task: kind now accepts 'issue'; new system_ids (set-semantics
associations) and arose_from_id (provenance, 0=unchanged/-1=clear) args.
create_note/update_note: new system_ids arg (notes associate with systems too).
services/notes.create_note: arose_from_id passthrough (update_note already
handles it via setattr).

Tests: MCP system tools + create_task issue-wiring (kind/provenance/systems),
service layer mocked.

Refs plan 825 (S2).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

src/scribe/mcp/tools/notes.py

@@ -15,6 +15,7 @@ from __future__ import annotations
 
 from scribe.mcp._context import current_user_id
 from scribe.services import notes as notes_svc
+from scribe.services import systems as systems_svc
 from scribe.services import trash as trash_svc
 
 
@@ -68,6 +69,7 @@ async def create_note(
     body: str = "",
     tags: list[str] | None = None,
     project_id: int = 0,
+    system_ids: list[int] | None = None,
 ) -> dict:
     """Create a new note in Scribe.
 
@@ -76,6 +78,8 @@ async def create_note(
         body: Markdown content. Supports [[wikilinks]] to other notes by title.
         tags: List of plain-string tags without # prefix, e.g. ["python", "ideas"].
         project_id: Associate with a project (use 0 for no project / orphan note).
+        system_ids: Ids of the project's Systems to associate this note with
+            (e.g. research about a subsystem). See list_systems / create_system.
 
     Returns the created note object including its assigned id.
     """
@@ -87,7 +91,14 @@ async def create_note(
         tags=tags,
         project_id=project_id or None,
     )
-    return note.to_dict()
+    if system_ids:
+        await systems_svc.set_record_systems(uid, note.id, system_ids)
+    data = note.to_dict()
+    if system_ids:
+        data["systems"] = [
+            s.to_dict() for s in await systems_svc.list_record_systems(uid, note.id)
+        ]
+    return data
 
 
 async def update_note(
@@ -96,6 +107,7 @@ async def update_note(
     body: str = "",
     tags: list[str] | None = None,
     project_id: int = 0,
+    system_ids: list[int] | None = None,
 ) -> dict:
     """Update an existing Scribe note. Only explicitly provided fields are changed.
 
@@ -105,6 +117,8 @@ async def update_note(
         body: New markdown body, or omit to leave unchanged.
         tags: Replaces the full tag list. Pass [] to clear all tags. Omit to leave unchanged.
         project_id: New project association. Omit (or pass 0) to leave unchanged.
+        system_ids: Replace this note's System associations with these ids
+            (set-semantics). None = leave unchanged; [] = clear all.
     """
     uid = current_user_id()
     fields: dict = {}
@@ -119,7 +133,14 @@ async def update_note(
     note = await notes_svc.update_note(uid, note_id, **fields)
     if note is None:
         raise ValueError(f"note {note_id} not found")
-    return note.to_dict()
+    if system_ids is not None:
+        await systems_svc.set_record_systems(uid, note_id, system_ids)
+    data = note.to_dict()
+    if system_ids is not None:
+        data["systems"] = [
+            s.to_dict() for s in await systems_svc.list_record_systems(uid, note_id)
+        ]
+    return data
 
 
 async def delete_note(note_id: int) -> dict: