refactor: eradicate deprecated tools (sticky_notes, pinned_files, context_workspaces, pr_checklist, preferences) and dead code

README.md

@@ -29,20 +29,16 @@ To prevent graph fragmentation and ensure optimal LLM tokenization and retrieval
 
 ## 🛠️ Consolidated Smart MCP Tools
 
-The server consolidates granular single-purpose tools into 12 concise, action-oriented smart domain handlers with zero prefix clutter:
+The server consolidates granular single-purpose tools into 8 concise, action-oriented smart domain handlers with zero prefix clutter:
 
 * **`tasks`**: Complete task lifecycle management (`add`, `update`, `delete`, `list`, `set_criteria`, `verify`).
 * **`milestones`**: Milestone tracking (`add`, `update`, `list`).
-* **`sticky_notes`**: Ephemeral scratchpad notes with TTL (`add`, `read`, `delete`, `clear`).
 * **`handoff_memos`**: Cross-session handoff notes (`leave`, `read`, `clear`).
-* **`pinned_files`**: Working set file focus management (`pin`, `unpin`, `list`).
-* **`context_workspaces`**: Workspace context state snapshots (`save`, `load`, `list`, `delete`, `diff`).
-* **`pr_checklist`**: Pre-commit and PR checklist management (`add`, `get`, `clear`).
 * **`snippets`**: Reusable code snippet vault with BM25+Vector search (`store`, `search`, `delete`, `tag`).
 * **`decisions`**: Architectural Decision Records (ADRs) (`log`, `query`, `delete`).
 * **`tech_debt`**: Engineering technical debt backlog (`log`, `resolve`, `list`).
 * **`environment`**: Infrastructure & tool fingerprints tracking (`update_fingerprint`, `read_fingerprint`, `log_requirement`, `register`, `get_details`).
-* **`clipboard`**: Cross-OS clipboard management (`read`, `write`, `toggle_watch`).
+* **`clipboard`**: Cross-OS clipboard management (`read`, `write`).
 
 ---
 
@@ -86,9 +82,6 @@ Evaluates task dependency graphs and returns unblocked, ready-to-run tasks for s
 ### 🧠 Chain-of-Thought & Diagnostic Hypothesis Memory (`log_hypothesis` / `query_hypotheses`)
 Records structured diagnostic hypotheses, test evidence, and verification statuses to preserve reasoning across sessions.
 
-### 🔀 Context Workspace Diffing (`context_workspaces`)
-Computes structured diffs of pinned files and active task IDs between two saved context workspaces.
-
 ### 🔒 Resilient Storage & Serde Parameter Tolerances
 * **Explicit Fail-Fast Persistence Safety**: Replaced unsafe silent fallback to temporary databases (`/tmp/mcp_store_fallback_*`) with an explicit open retry and fail-fast panic unless `MCP_ALLOW_TMP_FALLBACK=1` is explicitly set, preventing silent data loss.
 * **Store Write Lock Minimization**: Releases write lock immediately following in-memory mutation, serializing JSON payloads under read locks to allow non-blocking concurrent readers.