doc: Document the current system and clean up outdated documentation

[NhanLuongBGSV]

Summary

Document the current state of the system and clean up documentation that is no longer accurate.

The docs/ directory currently holds ~42 markdown files across architecture, getting-started, guides, principles, reference, and examples. Some of these are out of sync with the actual codebase (see existing open issues #544, #543, #542 — incomplete/miscounted Plugin API reference, invalid build command, obsolete deployment guide).

Goals

• Audit existing docs against the current codebase to identify outdated or incorrect content.
• Update / rewrite the affected sections so they reflect how the system works today.
• Remove docs that describe removed features or deprecated behavior.
• Ensure the getting-started / deployment guides are usable end-to-end on a fresh checkout.

Scope

• docs/ tree (architecture, getting-started, guides, principles, reference, examples).
• Cross-reference and resolve the already-open doc issues (doc: The main deployment guide is obsolete and its quickstart is unusable #542, doc: The documented plugin build command is invalid #543, doc: The Plugin API reference is incomplete and miscounts its own methods #544) where they overlap.

Out of scope

• New features (purely a documentation pass).