docs: address copilot feedback (ToC links, hierarchy, config cleanup)

[lan17]

Address feedback from #9

[Copilot]

Pull request overview

This PR addresses documentation feedback by updating the Table of Contents links, fixing heading hierarchy, and cleaning up configuration examples.

Changes:

• Updated ToC links for Install, Configure, Run, and Docker sections
• Changed "CLI" to "Commands" in ToC
• Removed duplicate EMAIL_KEY from environment variable example
• Fixed heading hierarchy for "Extensible by design" section

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[Copilot]

These ToC links won't work because they reference anchors that don't exist. The targets 2. **Install**, 3. **Configure**, and 4. **Run** are numbered list items under the "Manual Setup" section, not markdown headings. Markdown only generates anchor links from headings (lines starting with #).

Consider either: (1) converting these list items to proper headings (e.g., ### 2. Install), or (2) updating the ToC to link to the parent section #manual-setup instead, or (3) removing these ToC entries since they're sub-items of the Quickstart section.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 72.77%. Comparing base (f417abc) to head (945957f).
⚠️ Report is 2 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main      #15   +/-   ##
=======================================
  Coverage   72.77%   72.77%           
=======================================
  Files          59       59           
  Lines        4849     4849           
=======================================
  Hits         3529     3529           
  Misses       1320     1320           

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