feat: Self-modification engine — backend wiring and API

[Steake]

PR #41 implements a self-modification UI but the backend wiring — the actual self-modification engine that the UI is intended to drive — is either dormant or absent.

Scope

• Audit godelOS/ for self-modification primitives
• Implement or activate the backend engine
• Expose via internal API consumed by the UI in Self modification UI #41
• Write tests

Acceptance criteria

Self-modification operations initiated via UI produce verifiable changes to the knowledge graph or active reasoning modules.

Milestone: v0.5