refactor: migrate .runpod directory to .flash (AE-2257)

Rename all references from .runpod to .flash across the codebase:
- Update CLI commands, docs, and skeleton templates
- Update .gitignore and .flashignore patterns
- Update ResourceManager config directory path
- Update test fixtures and conftest helpers
- Remove obsolete scanner tests for deleted .runpod patterns

Author: deanq