Fix Prettier formatting in docs from #41

[walidabualafia]

Summary

• Whitespace-only formatting fixes (table alignment, trailing spaces) in 5 doc files
• These files were edited in PR Fix outdated documentation for merged PRs #2, #9, #13, #15, #17 #41 but pnpm format was not run before pushing, causing the format CI check to fail

Files changed

All changes are whitespace-only (Prettier table column alignment):

• README.md
• docs/guide/tools.md
• docs/reference/cli.md
• docs/reference/configuration.md
• docs/reference/security.md

Test plan

• pnpm format:check passes locally
• pnpm build passes
• pnpm lint passes
• pnpm test passes (96/96)
• Secret scan clean

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