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

.agents/skills/lint/SKILL.md

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+---
+name: Lint and Format Code
+description: Instructions for checking code style and formatting using Ruff.
+---
+
+# Skill: Lint and Format Code
+
+The goal of this skill is to enforce the project's adherence to the Google style standard and to maintain high code quality across the python source files.
+
+## Instructions
+
+1. **Format Code**: To automatically format all Python files according to the `ruff.toml` specifications:
+   ```bash
+   uv run ruff format .
+   ```
+
+2. **Check for Lints / Auto-fix**: To check the repository for style violations and automatically fix safe corrections:
+   ```bash
+   uv run ruff check --fix .
+   ```
+
+## Important Considerations
+- The `ruff.toml` file at the root handles all lint and format configuration. Do not ignore configurations when applying fixes.
+- If Ruff points out complex errors that cannot be auto-fixed, analyze the code and manually address the violations, prioritizing descriptive naming and adherence to the single-responsibility principle.

.agents/skills/test/SKILL.md

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+---
+name: Run Tests
+description: Instructions for executing the project test suite to verify code correctness.
+---
+
+# Skill: Run Tests
+
+The goal of this skill is to verify that the project is functioning correctly after development changes. 
+
+## Instructions
+
+1. **Verify Environment**: The project operates dynamically with hardware acceleration (GPU via JAX) and uses `uv` for dependency/execution management.
+2. **Execute Tests**:
+   - To run basic verification (e.g., checking JAX initialization and hardware detection), run the test script:
+     ```bash
+     uv run python -m tests.test_jax_init
+     ```
+   - If a broader suite of modular tests is added (e.g., `pytest`), execute tests in the `tests/` directory with:
+     ```bash
+     uv run pytest tests/
+     ```
+
+## Important Considerations
+- If you are running tests inside the local environment without a Devcontainer, verify whether `uv sync --frozen` (for CPU) or `uv sync --frozen --extra cuda` (for GPU) has been executed to avoid import errors.
+- Do not run bare `python ...` without `uv run` locally, unless you are strictly operating inside a pre-activated `.venv` inside a Devcontainer.