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

agent-rules/mcp_memory_workflow.md

@@ -16,8 +16,8 @@ description: Strict guidelines for interacting with the mcp-memory server, ensur
 > 2. **Tier 2 (Structured DB & Telemetry)**: The MCP Memory server specializes in high-volume, dynamic data: file modification ledgers (`audit_ledger`), terminal command history, error resolutions (`log_error_fix`), active tasks, and preflight context aggregation.
 
 The MCP Memory server is the central brain. You must be PROACTIVE, not reactive, in using it:
-- **Session Starts & Context Drops**: Always begin by calling `tasks` (action: "list"), `pinned_files` (action: "list"), and `sticky_notes` (action: "read"). 
-- **Sticky Notes**: Use `sticky_notes` (action: "add") for transient, session-scoped operational constraints (e.g., "Do not touch file X until Y is done"). Deletion supports both 1-based index (standard) and 0-based index 0.
+- **Session Starts & Context Drops**: Always begin by calling `tasks` (action: "list"), `get_preflight_context`, and `omni_search` to regain context.
+- **Context Switching**: When switching tasks or branches, use `manage_checkpoint` (action: "create") to freeze state, and use `manage_checkpoint` (action: "restore") to restore state for the task.
 - **Error Fixes**: The moment a tricky, undocumented, or environment-specific bug is resolved (e.g., Bitbucket markdown rendering quirks, nuanced framework bugs), IMMEDIATELY call `log_error_fix`. Supply `repo_name`, `error_category`, and `stack_trace` so future searches can perform embedding-based match.
 - **Tech Debt**: If you notice an anti-pattern (e.g., nested `if` statements, arrow anti-pattern) but deliberately skip fixing it to focus on a feature, IMMEDIATELY call `tech_debt` (action: "log") with `description`, `file_path`, `line_range`, `workaround`, `effort_estimate`, and `severity`.
 - **Architectural Decisions (ADR)**: When selecting design patterns, crate choices, or system structure, call `decisions` (action: "log") with `author`, `affected_components`, `alternatives_considered`, `decision`, and `consequence`.