Update CLI log-cleaning function to preserve files if present

[Harjun751]

What is the purpose of this pull request?

• Documentation update
• Bug fix
• Feature addition or enhancement
• Code maintenance
• DevOps
• Improve developer experience
• Others, please explain:

This is a re-PR over #2810.
Wanted to try out cherry-picking, and that PR had a lot of visual noise from my repeated poking of Copilot.

Resolves #2767

Overview of changes:
Update CLI clean functionality to use rmdir instead of a force delete. This preserves the folder structure in the situation where files already exist in them. Added test cases to account for this case.

Anything you'd like to highlight/discuss:
There is one instance in the cliUtil where I use console.warn to print out a warning message. It should only occur when the system fails to delete an empty directory for an unexpected reason (e.g. permissions). I specifically use console because it felt odd to me to import and create a new instance of logger (which we're cleaning up after in that context...).

Relevant snippet:

try {
    fs.rmdirSync(pathName);
  } catch (error) {
    // If directory is not empty, fail silently
    if (error.code !== DIR_NOT_EMPTY_ERROR_CODE) {
      // Warn for other unexpected errors
      // Use `console` instead of logger as we don't want to create a new logger instance
      // that might pollute the working directory again.
      // eslint-disable-next-line no-console
      console.warn(`WARNING: Failed to delete directory ${pathName}: ${error.message}`);
    }
  }

Testing instructions:

Proposed commit message: (wrap lines at 72 characters)

Update CLI clean function to preserve existing files

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Checklist: ☑️

• Updated the documentation for feature additions and enhancements
• Added tests for bug fixes or features
• Linked all related issues
• No unrelated changes

---

Reviewer checklist:

Indicate the SEMVER impact of the PR:

• Major (when you make incompatible API changes)
• Minor (when you add functionality in a backward compatible manner)
• Patch (when you make backward compatible bug fixes)

At the end of the review, please label the PR with the appropriate label: r.Major, r.Minor, r.Patch.

Breaking change release note preparation (if applicable):

• To be included in the release note for any feature that is made obsolete/breaking

Give a brief explanation note about:

• what was the old feature that was made obsolete
• any replacement feature (if any), and
• how the author should modify his website to migrate from the old feature to the replacement feature (if possible).

[codecov]

Codecov Report

❌ Patch coverage is 90.90909% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 71.85%. Comparing base (6da5bc9) to head (b2705a9).
⚠️ Report is 1 commits behind head on master.

Files with missing lines	Patch %	Lines
packages/cli/src/util/cliUtil.js	90.90%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2811      +/-   ##
==========================================
+ Coverage   71.83%   71.85%   +0.02%     
==========================================
  Files         134      134              
  Lines        7331     7340       +9     
  Branches     1622     1503     -119     
==========================================
+ Hits         5266     5274       +8     
- Misses       1937     2020      +83     
+ Partials      128       46      -82     

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[Copilot]

Pull request overview

This PR fixes a bug where MarkBind CLI creates a _markbind/logs directory during markbind serve that doesn't get cleaned up when the command fails on an invalid folder. The fix changes the cleanup strategy from force-deleting directories to using rmdir, which only removes empty directories, thereby preserving any existing user files.

Changes:

• Replaced fs.rmSync() with fs.rmdirSync() in a new tryDeleteFolder() helper function that silently skips non-empty directories
• Added comprehensive test cases covering empty directories, non-empty directories, and partial cleanup scenarios
• Included unrelated package-lock.json updates (peer dependency flags and optional encoding package)

Reviewed changes

Copilot reviewed 2 out of 3 changed files in this pull request and generated 2 comments.

File	Description
packages/cli/src/util/cliUtil.js	Introduced tryDeleteFolder() function using rmdirSync() to delete only empty directories, with error handling for non-empty directories
packages/cli/test/unit/cliUtil.test.js	Updated and added test cases to verify the new behavior of preserving non-empty directories during cleanup
package-lock.json	Contains numerous peer dependency flag changes and adds an optional encoding package (appears unrelated to the main fix)

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[gerteck]

LGTM, thanks @Harjun751

[github-actions]

@gerteck Each PR must have a SEMVER impact label, please remember to label the PR properly.