US-6.4.1: CLI `polysim run` command

[Peariforme]

User Story

As a CLI user, I want to launch a full simulation from a TOML config file.

Acceptance Criteria

• polysim run simulation.toml
• Progress bar, ETA, real-time stats (T, P, E)
• Automatic checkpointing (resume after interruption)
• polysim continue checkpoint.bin