Add apply_seed agent tool

[ammar-s847]

Summary

• add TopologyWrite apply_seed tool for random, ring, small_world, and layered seeds
• add an engine actor ApplySeed command that persists through Cortex::apply_seed when a folder is open, otherwise seeds live memory
• verify a 200-node small-world seed is visible through graph_snapshot

Tests

• cargo test -p core

Stacked on #51. Closes #17