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>

README.md

@@ -14,7 +14,7 @@ MCP Agents  ──MCP/HTTP──▶ MCP Server (Docker) ──┘
 
 - **Engine**: Keeps the embedding model warm in memory. Handles search, ingestion, document management, and note mutation via REST API. Runs in Docker with NVIDIA GPU, AMD GPU (ROCm), or CPU-only support.
 - **Client**: Single static Go binary. No Python, no ML dependencies, instant startup. Talks to the engine over HTTP.
-- **MCP Server**: Exposes kb operations as native MCP tools over Streamable HTTP. Runs as a separate Docker container alongside the engine. Supports collections for scoping agent memory vs user documents.
+- **MCP Server**: Exposes kb operations as native MCP tools over Streamable HTTP. Runs as a separate Docker container alongside the engine. Use tags to scope agent data from user documents.
 - **Storage**: Single SQLite database with FTS5 (keyword search) and sqlite-vec (vector search). Portable via bind mount — just copy the data directory between hosts.
 
 ## Quick start
@@ -149,6 +149,11 @@ kb tag 1 --add important
 kb export 1 -o manual.pdf    # download original file
 kb remove 3 --yes
 kb status
+
+# Bulk operations
+kb bulk-remove --tags "draft,old" --type note --yes
+kb bulk-tag --type note --add "archived" --yes
+kb bulk-set-tags --tags "old-scheme" --set "new-scheme" --yes
 ```
 
 ## How it works
@@ -192,7 +197,7 @@ Data is device-agnostic — you can ingest on NVIDIA and serve from AMD or CPU (
 
 The MCP server exposes kb operations as native MCP tools over Streamable HTTP, so agents can search, add notes, upload files, and manage documents without shelling out to the CLI. Includes setup guides for Claude Code, VS Code, Cursor, Windsurf, and JetBrains IDEs.
 
-See **[MCP.md](MCP.md)** for full details — server setup, available tools, collections, configuration, and client examples.
+See **[MCP.md](MCP.md)** for full details — server setup, available tools, tag-based organisation, configuration, and client examples.
 
 ## Agent skill