Add bulk operations and remove collections abstraction

- Add bulk delete, bulk tags, and bulk set-tags engine endpoints
  (POST /api/v1/bulk/delete, /bulk/tags, /bulk/set-tags)
- Filter-based selection: by tags, doc_type, ID list, ID range
- Safety threshold (KB_BULK_SAFETY_PERCENT, default 70%) prevents
  accidental mass operations unless force=true
- Synchronous execution with audit trail via jobs table
- Add kb_bulk_delete, kb_bulk_tags, kb_bulk_set_tags MCP tools
- Add kb bulk-remove, bulk-tag, bulk-set-tags CLI commands
- Remove collection abstraction from MCP server (use tags instead)
- Remove kb_set_collection MCP tool
- Update SKILL.md, MCP.md, README.md documentation

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

mcp/engine.py

@@ -106,6 +106,93 @@ def update_tags(doc_id: int, add: list[str] | None = None,
         return r.json()
 
 
+def delete_document(doc_id: int) -> dict:
+    with _client() as c:
+        r = c.delete(f"/api/v1/documents/{doc_id}")
+        r.raise_for_status()
+        return r.json()
+
+
+def _bulk_body(
+    document_ids: list[int] | None = None,
+    tags: list[str] | None = None,
+    doc_type: str | None = None,
+    from_id: int | None = None,
+    to_id: int | None = None,
+    force: bool = False,
+    **extra,
+) -> dict:
+    body: dict = {}
+    if document_ids:
+        body["document_ids"] = document_ids
+    if tags:
+        body["tags"] = tags
+    if doc_type:
+        body["doc_type"] = doc_type
+    if from_id is not None:
+        body["from_id"] = from_id
+    if to_id is not None:
+        body["to_id"] = to_id
+    if force:
+        body["force"] = True
+    body.update(extra)
+    return body
+
+
+def bulk_delete(
+    document_ids: list[int] | None = None,
+    tags: list[str] | None = None,
+    doc_type: str | None = None,
+    from_id: int | None = None,
+    to_id: int | None = None,
+    force: bool = False,
+) -> dict:
+    body = _bulk_body(document_ids, tags, doc_type, from_id, to_id, force)
+    with _client() as c:
+        r = c.post("/api/v1/bulk/delete", json=body)
+        r.raise_for_status()
+        return r.json()
+
+
+def bulk_tags(
+    document_ids: list[int] | None = None,
+    tags: list[str] | None = None,
+    doc_type: str | None = None,
+    from_id: int | None = None,
+    to_id: int | None = None,
+    add: list[str] | None = None,
+    remove: list[str] | None = None,
+    force: bool = False,
+) -> dict:
+    extra = {}
+    if add:
+        extra["add"] = add
+    if remove:
+        extra["remove"] = remove
+    body = _bulk_body(document_ids, tags, doc_type, from_id, to_id, force, **extra)
+    with _client() as c:
+        r = c.post("/api/v1/bulk/tags", json=body)
+        r.raise_for_status()
+        return r.json()
+
+
+def bulk_set_tags(
+    document_ids: list[int] | None = None,
+    tags: list[str] | None = None,
+    doc_type: str | None = None,
+    from_id: int | None = None,
+    to_id: int | None = None,
+    new_tags: list[str] | None = None,
+    force: bool = False,
+) -> dict:
+    extra = {"new_tags": new_tags or []}
+    body = _bulk_body(document_ids, tags, doc_type, from_id, to_id, force, **extra)
+    with _client() as c:
+        r = c.post("/api/v1/bulk/set-tags", json=body)
+        r.raise_for_status()
+        return r.json()
+
+
 def upload_file(filename: str, file_bytes: bytes,
                 tags: list[str] | None = None) -> dict:
     fields: dict = {}