fix(cli): integrate checkpoint resume

[Jaswanth-Sriram-Veturi]

Fixes #1249

Problem

The CLI accepted --checkpoint, but run_analysis() directly streamed a graph compiled without a checkpointer or stable
thread_id. Crashed CLI runs therefore could not resume.

Changes

• Configure the SQLite checkpointer on the CLI streaming path.
• Propagate the deterministic checkpoint thread_id.
• Pass None when resuming so completed nodes are not replayed.
• Clear checkpoints after successful completion.
• Close the checkpointer in finally.
• Expose checkpoint lifecycle methods as public graph methods because the CLI uses them.
• Add a regression test that asserts completed nodes execute only once across crash and resume.