Refactor package topology toward canonical cli/cases/data/models/training/runtime layout

[xiao312]

Summary

• add package-topology spec and staged migration docs
• introduce canonical packages for cli, cases, data, models, training, and runtime
• keep legacy import paths as compatibility shims during migration
• split pure HDF5 I/O helpers into a canonical data package slice
• move runtime helpers into a canonical runtime package slice
• move model/training code toward canonical package boundaries
• keep CLI behavior and command names stable while migrating internal package paths

Main changes

• dfode_kit/cli/ added; dfode_kit/cli_tools/ retained as shim layer
• dfode_kit/cases/ added; dfode_kit/df_interface/ retained as shim layer
• dfode_kit/data/ added with contracts and HDF5 I/O helpers
• dfode_kit/models/ and dfode_kit/training/ added
• dfode_kit/runtime/ added; runtime_config.py retained as shim
• docs updated to describe canonical vs legacy transitional paths

Verification

• make bootstrap-harness
• make verify
• make docs-build

Integrated verification passed with 44 tests passing.