chore: rework agent rules and skills to use standard .agents directory

.agents/rules/general.md

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+# General AI Agent Rules
+
+When assisting with this project, the AI Agent must strictly abide by these overarching operational rules:
+
+## 1. Scientific Integrity
+- **No Hallucinations**: You must never fabricate results, hallucinate citations, or generate false empirical claims. Do not guess what happened if a process fails; rely strictly on outputs and logs.
+
+## 2. Agent Operational Constraints
+- **Absolute Paths**: Always use absolute paths when making tool calls or reading/writing files.
+- **Refactoring Guardrails**: Do not commence massive files/directory refactors or major system migrations without explicitly communicating the plan and asking for user clarification or approval first.
+- **No Boilerplate Feedback**: The AI must not produce generic boilerplate summaries or overly generic advice. Ensure all outputs are completely contextual, robust, and well-reasoned.
+
+## 3. Communication
+- **Artifacts and UI**: Use artifacts (like `implementation_plan.md` or `task.md`) appropriately for tracking design phases and updates.
+- **Explicit Documenting**: If performing design choices, list them explicitly. Keep the output focused on the exact task.