List mu-plugins from subfolders

[Copilot]

Implementation Complete: Add support for listing mu-plugins from subfolders

• Understand the current implementation of get_all_items() in Plugin_Command.php
• Modify get_all_items() to also fetch plugins from mu-plugins subfolders using get_plugins()
• Ensure the subfolder mu-plugins are displayed with "must-use" status
• Create a test scenario to validate the change
• Run static analysis and code style checks - all passing
• Address code review feedback - refactored with array_replace for better readability
• Run security analysis - no issues found

Summary

This PR adds support for listing must-use plugins located in subfolders within the mu-plugins directory. Many WordPress sites use mu-plugin loaders like Bedrock Autoloader or WPStarter MULoader to load plugins from subfolders. These plugins are displayed in the WP admin backend but were not being listed by wp plugin list before this change.

Changes Made:

• Modified Plugin_Command::get_all_items() to fetch plugins from mu-plugins subfolders using the standard WordPress approach: get_plugins( '/../' . basename( WPMU_PLUGIN_DIR ) )
• Used array_replace() to merge root-level and subfolder mu-plugins with proper precedence
• All subfolder mu-plugins are marked with "must-use" status to match WordPress behavior
• Added Behat test scenario "Listing mu-plugins should include plugins from subfolders"
• Refactored for better readability with descriptive variable names

Testing:

• All lint checks pass ✅
• PHPCS code style checks pass ✅
• PHPStan static analysis passes ✅
• CodeQL security analysis - no issues ✅
• New test scenario added to validate functionality ✅

Code Quality:

• Minimal changes (3 lines of new code + test)
• Clear, concise implementation using array_replace()
• Descriptive variable names for better code clarity
• No breaking changes to existing functionality
• Follows WordPress coding standards

Original prompt

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This section details on the original issue you should resolve

<issue_title>Listing folders in mu-plugins</issue_title>
<issue_description>A lot of more complex sites make use of subfolders in the muplugins folder, just like with regular plugins.

They then use something like the Bedrock Autoloader or the MULoader in WPStarter.

Although these plugins are then active like normal plugins and properly shown in the WP admin backend, WP-CLI does not display them with plugin list.

To correctly mirror WP behaviour, these should be shown as well if they are active.</issue_description>

<agent_instructions>Plugin_Command::get_all_items() could use get_plugins( '/../' . basename( WPMU_PLUGIN_DIR ) ) and add those plugins to the list.</agent_instructions>

Comments on the Issue (you are @copilot in this section)

• Fixes Listing folders in mu-plugins #25

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