refactor: give Agents API its own source tree

[chubes4]

Goal

Give Automattic/agents-api its own source-tree shape instead of preserving the Data Machine extraction layout.

Current smell

The standalone repo currently mirrors the old Data Machine module layout:

inc/Core/FilesRepository/*
inc/Core/Database/Chat/*
inc/AI/*
inc/class-wp-agent-package-*.php

That reads like Data Machine internals copied into a repo, not a standalone Agents API substrate.

Desired direction

Move toward an agent-native tree, for example:

src/
  Registry/
  Runtime/
  Tools/
  Memory/
  Transcripts/
  Packages/

Exact naming can differ if the implementation supports a cleaner WordPress convention, but the shape should use Agents API vocabulary rather than Data Machine storage/backend vocabulary.

Scope

• Move files and update bootstrap/test paths.
• Preserve public API names and behavior.
• Preserve global WordPress-shaped facades such as WP_Agent, WP_Agents_Registry, and wp_register_agent().
• Preserve namespaced public contracts unless the rename is purely path-level and low-risk.
• Update smoke tests so they pin the new layout and still prove no Data Machine imports leak in.

Out of scope

• No Data Machine dependency changes in this PR.
• No REST/admin/runtime feature additions.
• No compatibility alias ladder back to old paths/classes unless a concrete failing consumer proves it is needed.

Acceptance criteria

• composer test passes.
• Bootstrap loads all moved files from the new tree.
• Source tree no longer contains Core/FilesRepository or Core/Database/Chat as the primary public layout.
• PR body includes AI assistance disclosure.