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/systems.py

@@ -0,0 +1,150 @@
+"""System CRUD + record-association MCP tools — wrappers over services/systems.py.
+
+A System is a per-project, reusable, self-describing subsystem/area that any
+record (note, task, or issue) can be associated with — so research, build-work,
+and corrective work line up under the same area and recurring problem-spots are
+visible. The service enforces the multi-user ACL (project permission); these
+tools are thin wrappers.
+
+Sentinels (match the milestone/task tool conventions):
+  - name="" / description="" / color="" / status="" → "leave unchanged" on update
+  - order_index=-1 → "leave unchanged" on update (0 is a valid order_index)
+"""
+from __future__ import annotations
+
+from scribe.mcp._context import current_user_id
+from scribe.services import systems as systems_svc
+
+
+async def create_system(
+    project_id: int,
+    name: str,
+    description: str = "",
+    color: str = "",
+) -> dict:
+    """Create a System (a reusable, self-describing subsystem/area) in a project.
+
+    Associate records with it via the `system_ids` arg on create/update_task and
+    create/update_note.
+
+    Args:
+        project_id: The project this system belongs to (required).
+        name: Short label (required).
+        description: What the system is and how it's used — a name is rarely enough.
+        color: Optional UI accent (hex), or empty.
+    """
+    uid = current_user_id()
+    system = await systems_svc.create_system(
+        uid, project_id=project_id, name=name,
+        description=description or None, color=color or None,
+    )
+    if system is None:
+        raise ValueError(f"cannot create system in project {project_id} (no write access)")
+    return system.to_dict()
+
+
+async def list_systems(project_id: int, include_archived: bool = False) -> dict:
+    """List a project's systems (active by default), ordered by order_index.
+
+    Pass include_archived=True to include archived systems.
+    """
+    uid = current_user_id()
+    rows = await systems_svc.list_systems(uid, project_id, include_archived=include_archived)
+    return {"systems": [s.to_dict() for s in rows]}
+
+
+async def get_system(system_id: int) -> dict:
+    """Fetch a System plus the records associated with it.
+
+    Returns the system, plus its associated records split into `issues`,
+    `tasks` (work/plan), and `notes`.
+    """
+    uid = current_user_id()
+    system = await systems_svc.get_system(uid, system_id)
+    if system is None:
+        raise ValueError(f"system {system_id} not found")
+    records = await systems_svc.list_records_for_system(uid, system_id)
+    issues, tasks, notes = [], [], []
+    for r in records:
+        d = r.to_dict()
+        if r.status is None:
+            notes.append(d)
+        elif r.task_kind == "issue":
+            issues.append(d)
+        else:
+            tasks.append(d)
+    data = system.to_dict()
+    data["issues"] = issues
+    data["tasks"] = tasks
+    data["notes"] = notes
+    return data
+
+
+async def update_system(
+    system_id: int,
+    name: str = "",
+    description: str = "",
+    color: str = "",
+    status: str = "",
+    order_index: int = -1,
+) -> dict:
+    """Update a System. Only explicitly provided fields change.
+
+    Args:
+        status: 'active' or 'archived'. Archive a system to retire it without
+            losing history; archived systems hide from default lists.
+        order_index: display position (0-based); -1 = leave unchanged.
+    """
+    uid = current_user_id()
+    fields: dict = {}
+    if name:
+        fields["name"] = name
+    if description:
+        fields["description"] = description
+    if color:
+        fields["color"] = color
+    if status:
+        fields["status"] = status
+    if order_index >= 0:
+        fields["order_index"] = order_index
+    system = await systems_svc.update_system(uid, system_id, **fields)
+    if system is None:
+        raise ValueError(f"system {system_id} not found or no write access")
+    return system.to_dict()
+
+
+async def list_system_records(
+    system_id: int, kind: str = "", open_only: bool = False
+) -> dict:
+    """List records associated with a System.
+
+    Args:
+        kind: filter by task_kind — 'issue', 'work', or 'plan'. Omit for all.
+        open_only: limit to tasks not done/cancelled (e.g. open issues only).
+    """
+    uid = current_user_id()
+    rows = await systems_svc.list_records_for_system(
+        uid, system_id, kind=kind or None, open_only=open_only,
+    )
+    return {"records": [r.to_dict() for r in rows]}
+
+
+async def delete_system(system_id: int) -> dict:
+    """Soft-delete a System (recoverable). Its record associations are removed."""
+    uid = current_user_id()
+    ok = await systems_svc.delete_system(uid, system_id)
+    if not ok:
+        raise ValueError(f"system {system_id} not found or no write access")
+    return {"message": f"System {system_id} deleted."}
+
+
+def register(mcp) -> None:
+    for fn in (
+        create_system,
+        list_systems,
+        get_system,
+        update_system,
+        list_system_records,
+        delete_system,
+    ):
+        mcp.tool(name=fn.__name__)(fn)