refactor: rename directories for clarity (agent_patterns, agentcore_gateway, agentcore_tools)

Naming improvements to make the repo structure clearer.

1. `patterns/` → `agent_patterns/`: Renaming to `agent_patterns/` makes it immediately clear that this is where agent code lives.
2. `gateway/` → `agentcore_gateway/` and `tools/` → `agentcore_tools/`: Prefixing with `agentcore_` makes it clear these are AgentCore-specific features, not general-purpose utilities.

**Files to update**: All references to the old paths in: `infra-cdk/`, `infra-terraform/`, `docs/`, `scripts/`, `test-scripts/`, `Makefile`, `pyproject.toml`, `.dockerignore`, `docker/`, `config.yaml`.