refactor: centralize tool plugin hooks + add agent to hook input

[ArmirKS]

Description

prompt.ts has the same before/after plugin hook logic inline in 3 separate places, and none of them pass agent to the hooks. This means plugins can't tell which agent made a tool call — a blocker for any plugin that needs per-agent policy (audit logging, permission enforcement, etc).

Steps to reproduce

1. Create a plugin that hooks tool.execute.before and logs the input
2. Trigger tool calls from different agents (primary + subagents via task)
3. Observe that the hook input has no agent field — the plugin can't distinguish who made the call

Fix

PR #13521 adds Tool.invoke() that centralizes hook wrapping and adds agent to the hook input.

The original batch bypass issue is moot since batch is experimental and being deprecated.