Convert legacy formatting to admonitions and add cross-reference anchors

[yomybaby]

Convert legacy documentation formatting patterns to modern admonition syntax and establish cross-reference anchor infrastructure across EN, JA, and TH documentation.

Why This Work is Needed

The documentation currently uses 3-space indented notes (a legacy convention) and inconsistent cross-reference link formats. These legacy patterns are harder to maintain, don't render with proper visual distinction, and break cross-references between sections. The documentation style guide recommends admonitions for new content, and this work completes the migration for existing content.

Expected Outcomes

• All 3-space indented notes converted to :::note or :::warning admonitions across EN, JA, TH docs
• ~100 HTML anchor tags added for stable cross-reference targets
• 20+ cross-reference links fixed from legacy format to standard markdown anchors
• Duplicate H1 headings removed and broken markup fixed
• Indented code examples converted to proper fenced code blocks

JIRA Issue: FR-2086