refactor: eradicate deprecated tools (sticky_notes, pinned_files, context_workspaces, pr_checklist, preferences) and dead code
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@@ -90,11 +90,11 @@ The physical storage location of the knowledge graph and all persistent stores i
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## 10. Exposed MCP Capabilities (Tools)
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The server implements the Model Context Protocol (MCP) by exposing a vast suite of tools via the JSON-RPC interface, categorized broadly into:
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* **Graph Management:** create_entities, create_relations, merge_entities,
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ead_graph, etc.
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* **Task & Context Tracking:** add_task, add_sticky_note, add_session_summary, etc.
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* **Engineering & DevOps:** log_code_change, log_error_fix, log_tech_debt, add_pr_checklist_item.
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* **Environment & Workspaces:**
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egister_environment, save_context_workspace, pin_file.
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read_graph, etc.
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* **Task & Context Tracking:** tasks, milestones, handoff_memos, add_session_summary, etc.
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* **Engineering & DevOps:** log_code_change, log_error_fix, tech_debt, decisions, etc.
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* **Environment & Workspaces:** environment, manage_checkpoint, manage_subagent_namespace, snippets, etc.
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## 11. Concurrency & Thread Safety
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With the introduction of the Dual Transport System, the daemon must safely handle simultaneous read/write requests from both Stdio (Windows agy) and HTTP (WSL agy) clients.
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