docs: update CLI and configuration reference documentation

[yacosta738]

Update AgentSync documentation to accurately reflect CLI subcommands/flags for plugin and fix the Agent Compatibility Matrix table formatting and ordering.

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PR created automatically by Jules for task 11646960576976225525 started by @yacosta738

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[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: ASSERTIVE

Plan: Team

Run ID: c3375b0d-374d-4072-bda7-503bfe615044

📥 Commits

Reviewing files that changed from the base of the PR and between 7102a4d and 94cccc0.

📒 Files selected for processing (2)

• website/docs/src/content/docs/reference/cli.mdx
• website/docs/src/content/docs/reference/configuration.mdx

Included review availability: Your plan provides up to 1 included review per hour; 0 remain after this review.

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📝 Summary

Summary by CodeRabbit

• New Features

  • Added a --project-root option to the plugin command.
  • Added --json output options to plugin add, update, list, status, and remove commands.

• Documentation

  • Reordered the Agent Compatibility Matrix alphabetically.
  • Moved the Cursor rules filename note to immediately follow the compatibility table.

Walkthrough

The CLI reference now documents --project-root and --json plugin options. The configuration reference alphabetizes the Agent Compatibility Matrix and moves the Cursor rules filename note below the table.

Changes

Reference documentation

Layer / File(s)	Summary
CLI plugin option reference website/docs/src/content/docs/reference/cli.mdx	Documents the global --project-root option and --json for the add, update, list, status, and remove subcommands.
Agent compatibility matrix ordering website/docs/src/content/docs/reference/configuration.mdx	Alphabetizes matrix rows and moves the Cursor rules filename note after the table without changing row content.

Estimated code review effort: 1 (Trivial) | ~5 minutes

Merge Risk: ⚪ Minimal · up to 94ccc

This updates plugin option documentation and improves compatibility-matrix ordering without changing runtime behavior. No current merge-readiness risk remains.

Poem

A rabbit reads the flags at night
--json hops into sight
The project root finds its way
Matrix rows line up today
Cursor’s note rests after play

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check. Docstring coverage is scoped to functions touched by this diff. Analyzed 0 functions across 0…
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Description check	✅ Passed	The description accurately summarizes the CLI documentation updates and the Agent Compatibility Matrix changes.
Title check	✅ Passed	The title clearly and concisely identifies the documentation updates for the CLI and configuration reference.

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch docs/plugin-and-compatibility-matrix-fixes-11646960576976225525

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

📢 Thoughts on this report? Let us know!

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud