feat(appkit): migrate agent-app and docs to the new agents() plugin

[MarioCadenas]

Summary

Cuts over the reference application and documentation to the agents() plugin API introduced in PR #294.

Apps

• apps/agent-app/server.ts — rewritten from the deprecated createAgent({ plugins, tools, port }) app-shortcut to createApp({ plugins: [server(), analytics(), files(), agents({ agents: { support } })] }). The support agent is a code-defined createAgent(def) that spreads tools from the analytics and files plugins via .toolkit() and mixes in inline tool() + mcpServer() helpers.
• apps/agent-app/config/agents/assistant.md — rewritten to the new YAML frontmatter schema (proper --- delimiters, endpoint: / default: keys).

Docs

• docs/docs/plugins/agents.md — full guide for the new plugin. Covers the five progressive levels (markdown-only → frontmatter scoping → code-defined agents → sub-agents → standalone runAgent). Includes the configuration reference and the full frontmatter schema table.
• docs/docs/guides/migrating-to-agents-plugin.md — migration guide from the old createAgent shortcut to createApp + agents(). Covers name changes, frontmatter format differences, code migration examples.
• Docs sidebar + regenerated typedoc API reference.

CLI template

• template/appkit.plugins.json — plugin registry synced to include agents for databricks apps init --features agents scaffolding.

PR Stack

1. Shared types + Adapters — feat(appkit): add shared agent types and LLM adapter implementations #282
2. Tool types + MCP client — feat(appkit): add FunctionTool, HostedTool types and MCP client #283
3. Agent plugin core + ToolProvider implementations — feat(appkit): add agent plugin core and ToolProvider implementations #284
4. PluginContext mediator — feat(appkit): add PluginContext mediator for inter-plugin communication #285
5. createAgent + agent-app + docs (v1) — feat(appkit): add createAgent wrapper, agent-app, and API docs #286
6. Plugin context-binding separation — refactor(appkit): separate plugin context binding from plugin construction #293
7. agents() plugin + createAgent(def) + .toolkit() — feat(appkit): add agents() plugin, createAgent() factory, and .toolkit() #294
8. agent-app + docs migrated to agents() (this PR)
9. Relocate shared agent utilities — refactor(appkit): relocate shared agent utilities into plugins/agents #296
10. preparePlugins forwards eager instance — refactor(appkit): forward eager plugin instance through preparePlugins #297
11. fromPlugin() API — feat(appkit): add fromPlugin() for referencing plugin tools in code-defined agents #298
12. Retire deprecated agent() + createAgentApp — chore(appkit): remove deprecated agent() plugin and createAgentApp shortcut #299
13. Retire toPluginWithInstance + bug fixes — refactor(appkit): retire toPluginWithInstance; consolidate on fromPlugin + fix schema/routing bugs #300

Test plan

• agent-app boots, registers both the code-defined support agent and the markdown-loaded assistant agent, streams responses
• Docs build clean (pnpm docs:build)
• Typecheck clean

[MarioCadenas]

Superseded by the v2 6-PR stack:

1. Shared agent types + LLM adapters — feat(appkit): shared agent types and LLM adapter implementations #301
2. Tool primitives + ToolProvider surfaces — feat(appkit): tool primitives and ToolProvider surfaces on core plugins #302
3. Plugin infrastructure (attachContext + PluginContext) — feat(appkit): plugin infrastructure — attachContext + PluginContext mediator #303
4. agents() plugin + createAgent(def) + markdown-driven agents — feat(appkit): agents() plugin, createAgent(def), and markdown-driven agents #304
5. fromPlugin() DX + runAgent plugins arg + toolkit-resolver — feat(appkit): fromPlugin() DX, runAgent plugins arg, shared toolkit-resolver #305
6. Reference app + dev-playground + docs — feat(appkit): reference agent-app, dev-playground chat UI, docs, and template #306

The v2 stack reorganizes the same work so no PR ships API that a later PR deletes. Start at #301 for the new entry point. Branches from this older stack are preserved unchanged.