refactor(agent-input): unify prompt usage accounting

[cniska]

Motivation

prompt usage accounting was split across agent input, lifecycle prepare, and lifecycle usage estimation, which made /usage less reliable and harder to reason about

Summary

• centralize prompt budget accounting in createAgentInput with a dedicated prompt token budget helper
• keep systemPromptTokens and toolTokens authoritative from requested usage values
• remove prepare-phase usage mutation and rely on createAgentInput as the source of truth
• use PromptUsage values directly when building lifecycle prompt breakdown totals
• add regression tests for tool token reporting and over-budget system/tool reservation behavior

Fixes #195