refactor: consolidate hypotheses, agent_signals, and process_logs into action-based smart tools

design.md

@@ -21,7 +21,7 @@ The server hosts a rich Single Page Application (SPA) natively on the root route
 *   `GET /`: The Brain Monitor live HTML dashboard SPA.
 *   `GET /api/graph`: Returns the full node/edge topology for the interactive physics-simulated canvas.
 *   `GET /api/tasks` & `POST /api/tasks/{id}/complete`: Drives the actionable Kanban board.
-*   `GET /api/sticky` & `GET /api/search`: Powers the sticky notes tab and global fuzzy search UI.
+*   `GET /api/ledger` & `GET /api/search`: Powers the code change ledger and global fuzzy search UI.
 *   `GET /api/stats`: Returns a JSON snapshot of current entity, relation, task, and tech debt counts.
 
 ### Git & IDE Integration Endpoints
@@ -61,7 +61,7 @@ The daemon has completely eliminated raw JSON file sprawl and fragmented delta-f
 The system leverages a modular, thread-safe generic `Store<T>` abstraction that automatically transparently serializes and deserializes native Rust structs directly into the underlying `redb` tables.
 Currently implemented persistent stores include:
 *   **Audit Ledger & Tasks:** Tracks agent actions and active background tasks.
-*   **Context & Handoffs:** Sticky notes, Session Summaries, Handoff Memos, and Context Workspaces.
+*   **Context & Handoffs:** Session Summaries, Handoff Memos, Hypotheses, and Agent Signals.
 *   **Engineering Tracking:** ADRs (Architecture Decision Records), Snippets, Error Fixes, Tech Debt, and PR Checklists.
 *   **Environment State:** Pinned Files, Env Fingerprints, Milestones, and Environments.
 *   **Safety Gates:** Authorized execution gates (Push Safety).
@@ -91,7 +91,7 @@ The physical storage location of the knowledge graph and all persistent stores i
 The server implements the Model Context Protocol (MCP) by exposing a vast suite of tools via the JSON-RPC interface, categorized broadly into:
 *   **Graph Management:** create_entities, create_relations, merge_entities, 
 read_graph, etc.
-*   **Task & Context Tracking:** tasks, milestones, handoff_memos, add_session_summary, etc.
+*   **Task & Context Tracking:** tasks, milestones, handoff_memos, hypotheses, agent_signals, process_logs, add_session_summary, etc.
 *   **Engineering & DevOps:** log_code_change, log_error_fix, tech_debt, decisions, etc.
 *   **Environment & Workspaces:** environment, manage_checkpoint, manage_subagent_namespace, snippets, etc.