refactor: give Agents API its own source tree

[chubes4]

Summary

• Move Agents API source files into an agent-native src/ tree organized by Registry, Packages, Runtime, Tools, Memory, and Transcripts concerns.
• Preserve public WordPress facades and namespaced contract names while removing the copied Data Machine physical layout.

Changes

• Updated agents-api.php bootstrap paths to load from the new src/ tree.
• Moved files out of inc/Core/*, inc/AI/*, and top-level inc/ into Agents API vocabulary directories.
• Extended the bootstrap smoke test to assert the expected source directories and absence of the legacy copied layout.

Tests

• composer test

Closes #3

AI assistance

• AI assistance: Yes
• Tool(s): OpenCode (GPT-5.5)
• Used for: Refactoring and testing the Agents API source-tree layout under Chris's review.