v0.4.0: Refresh docs/examples after Go subtree move

[tazarov]

Goal

Update docs and examples so repository navigation reflects the new Go layout and Java/Go separation remains clear.

Scope

• Update README.md, AGENTS.md, and code map sections.
• Update example paths and commands where needed.
• Ensure GO_API_SURFACE.md references remain accurate.

Acceptance Criteria

• No stale paths in docs.
• New contributor path-to-code is clear.
• Build/test instructions still work as written.

[tazarov]

Tracked by umbrella #45 (v0.4.0 root-cleanup plan).

[tazarov]

Completed: CLAUDE.md architecture diagram and build instructions reflect the internal/runtime/ + internal/library/ layout. Code map and contributor paths updated.