docs: update README.md for CLI accuracy

[yacosta738]

This PR updates the README.md to accurately reflect the current state of the AgentSync CLI.

Changes:

• Updated the Usage section to include essential missing flags for several commands:
  • init: Added [--path <path>] and [--force].
  • apply: Added [--path <path>].
  • clean: Added [--path <path>].
  • status: Added [--project-root <path>] and [--json] to the main list for consistency.
  • doctor: Added [--project-root <path>].
• Verified that all supported agents and their configuration paths in the Supported Agents and MCP Support sections match the actual implementation in src/mcp.rs and src/agent_ids.rs.
• Ensured all claims in the README are verifiable against the codebase and existing tests.

No logic changes were made; this is a documentation-only update.

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PR created automatically by Jules for task 13448363500065147622 started by @yacosta738

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[coderabbitai]

📝 Walkthrough

Summary by CodeRabbit

• Documentation
  • Updated CLI command reference with new optional path and context arguments for init, apply, clean, status, and doctor commands
  • Added support for project root specification and JSON output format options
  • Improved command flexibility for different use cases and project configurations

Walkthrough

The pull request updates CLI command documentation in the README to reflect newly supported optional arguments (--path, --force, --project-root, --json) across multiple commands while preserving existing flags.

Changes

Cohort / File(s)	Summary
Documentation Updates README.md	Updated CLI command syntax examples to document new optional path-scoping flags (--path, --force) and project-root context arguments (--project-root, --json) for init, apply, clean, status, and doctor commands.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~5 minutes

Poem

Hop, hop! The CLI now shows,
With flags that help the workflow flows,
--path and --force, a cleaner way,
Documentation bright as day! 🐰✨

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title 'docs: update README.md for CLI accuracy' is specific and directly describes the main change—updating documentation to reflect current CLI behavior.
Description check	✅ Passed	The description is comprehensive and directly related to the changeset, detailing the specific CLI flags added to the README and verification steps taken.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

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✨ Finishing touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch docs/update-readme-accuracy-13448363500065147622

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[github-actions]

✅ Contributor Report

User: @yacosta738
Status: Passed (12/13 metrics passed)

Metric	Description	Value	Threshold	Status
PR Merge Rate	PRs merged vs closed	89%	>= 30%	✅
Repo Quality	Repos with ≥100 stars	0	>= 0	✅
Positive Reactions	Positive reactions received	9	>= 1	✅
Negative Reactions	Negative reactions received	0	<= 5	✅
Account Age	GitHub account age	3028 days	>= 30 days	✅
Activity Consistency	Regular activity over time	108%	>= 0%	✅
Issue Engagement	Issues with community engagement	0	>= 0	✅
Code Reviews	Code reviews given to others	346	>= 0	✅
Merger Diversity	Unique maintainers who merged PRs	3	>= 0	✅
Repo History Merge Rate	Merge rate in this repo	0.8108108108108109	>= 0	✅
Repo History Min PRs	Previous PRs in this repo	75	>= 0	✅
Profile Completeness	Profile richness (bio, followers)	90	>= 0	✅
Suspicious Patterns	Spam-like activity detection	1	N/A	❌

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_{Contributor Report evaluates based on public GitHub activity. Analysis period: 2025-02-10 to 2026-02-10}