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.md

@@ -27,25 +27,25 @@ docker run -d --name kb-mcp \
 
 | Tool | Description |
 |---|---|
-| `kb_search` | Hybrid search with optional collection/tag/type filters |
+| `kb_search` | Hybrid search with optional tag/type filters |
 | `kb_addnote` | Add a text note (queued for async ingestion) |
 | `kb_update_note` | Update an existing note in place |
 | `kb_get` | Get document details by ID or source path |
+| `kb_delete` | Permanently delete a document by ID |
 | `kb_status` | Engine health and statistics |
 | `kb_jobs` | Ingestion queue status |
 | `kb_upload_start` | Start a chunked file upload |
 | `kb_upload_chunk` | Upload a base64-encoded file chunk |
 | `kb_upload_finish` | Finish upload and submit for ingestion |
+| `kb_bulk_delete` | Delete multiple documents matching a filter |
+| `kb_bulk_tags` | Add/remove tags on multiple documents |
+| `kb_bulk_set_tags` | Replace all tags on multiple documents |
 
-## Collections
+## Organising with tags
 
-The MCP server supports **collections** — scoped document namespaces implemented via tag conventions. Use these to separate agent memory from user documents:
+Use tags to separate agent data from user documents. For example, an agent can tag all its notes with `agent:mybot` and filter by that tag when searching. This is a naming convention — configure it in your agent's system prompt. No special server-side enforcement is needed.
 
-- `documents` (default) — user-facing documents
-- `memory` — agent memory and preferences
-- `workspace` — working context
-
-Tools accept a `collection` parameter. The MCP server translates this to `collection:<name>` tags on the engine, and strips them from responses so agents see a clean `"collection": "memory"` field.
+Bulk tools accept filter-based selection (by tags, doc_type, ID list, or ID range) so agents can manage thousands of documents in a single call instead of looping. A safety threshold (default 70%) prevents accidental mass operations unless `force: true` is set.
 
 ## MCP server configuration