Add warning in wp plugin is-active for missing plugin files still in active_plugins

features/plugin-is-active.feature

@@ -0,0 +1,86 @@
+Feature: Check if a WordPress plugin is active
+
+  Background:
+    Given a WP install
+
+  Scenario: Check if an active plugin is active
+    When I run `wp plugin activate akismet`
+    Then STDOUT should contain:
+      """
+      Success:
+      """
+
+    When I run `wp plugin is-active akismet`
+    Then the return code should be 0
+
+  Scenario: Check if an inactive plugin is not active
+    When I run `wp plugin activate akismet`
+    Then STDOUT should contain:
+      """
+      Success:
+      """
+
+    When I run `wp plugin deactivate akismet`
+    Then STDOUT should contain:
+      """
+      Success:
+      """
+
+    When I try `wp plugin is-active akismet`
+    Then the return code should be 1
+
+  Scenario: Check if a non-existent plugin is not active
+    When I try `wp plugin is-active non-existent-plugin`
+    Then the return code should be 1
+
+  Scenario: Warn when plugin is in active_plugins but file does not exist
+    When I run `wp plugin activate akismet`
+    Then STDOUT should contain:
+      """
+      Success:
+      """
+
+    When I run `wp plugin is-active akismet`
+    Then the return code should be 0
+
+    # Remove the plugin directory
+    When I run `wp plugin path akismet --dir`
+    Then save STDOUT as {PLUGIN_PATH}
+
+    When I run `rm -rf {PLUGIN_PATH}`
+    Then the return code should be 0
+
+    # Now the plugin file is gone but still in active_plugins
+    When I try `wp plugin is-active akismet`
+    Then STDERR should contain:
+      """
+      Warning: Plugin 'akismet' is marked as active but the plugin file does not exist.
+      """
+    And the return code should be 1
+
+  Scenario: Warn when network-activated plugin is in active_sitewide_plugins but file does not exist
+    Given a WP multisite install
+
+    When I run `wp plugin activate akismet --network`
+    Then STDOUT should contain:
+      """
+      Success:
+      """
+
+    When I run `wp plugin is-active akismet --network`
+    Then the return code should be 0
+
+    # Remove the plugin directory
+    When I run `wp plugin path akismet --dir`
+    Then save STDOUT as {PLUGIN_PATH}
+
+    When I run `rm -rf {PLUGIN_PATH}`
+    Then the return code should be 0
+
+    # Now the plugin file is gone but still in active_sitewide_plugins
+    When I try `wp plugin is-active akismet --network`
+    Then STDERR should contain:
+      """
+      Warning: Plugin 'akismet' is marked as active but the plugin file does not exist.
+      """
+    And the return code should be 1

src/Plugin_Command.php

@@ -1348,6 +1348,10 @@ public function is_installed( $args, $assoc_args ) {
 	 *
 	 * Returns exit code 0 when active, 1 when not active.
 	 *
+	 * If the plugin does not exist but is still in WordPress's active plugins storage
+	 * (such as the active plugins option or the sitewide plugins option for network-activated plugins),
+	 * a warning will be emitted.
+	 *
 	 * ## OPTIONS
 	 *
 	 * <plugin>
@@ -1371,6 +1375,55 @@ public function is_active( $args, $assoc_args ) {
 		$plugin = $this->fetcher->get( $args[0] );
 
 		if ( ! $plugin ) {
+			// Plugin not found via fetcher, but it might still be in active_plugins option
+			// Check if it's in the active_plugins list
+			$input_name = $args[0];
+			// For network plugins: active_sitewide_plugins is an array where keys are plugin files and values are timestamps
+			// For regular plugins: active_plugins is an array of plugin file paths
+			$active_plugins = $network_wide ? get_site_option( 'active_sitewide_plugins', [] ) : get_option( 'active_plugins', [] );
+
+			// Ensure we have an array to work with
+			if ( ! is_array( $active_plugins ) ) {
+				$active_plugins = [];
+			}
+
+			// For network-wide plugins, extract the plugin files from the keys
+			if ( $network_wide ) {
+				$active_plugin_files = array_keys( $active_plugins );
+			} else {
+				$active_plugin_files = $active_plugins;
+			}
+
+			// Try to find a matching plugin file in active_plugins using the same logic as the fetcher
+			// This matches: exact file name, "name.php", or directory name
+			$found_in_active = '';
+			foreach ( $active_plugin_files as $plugin_file ) {
+				// Ensure plugin_file is a string
+				if ( ! is_string( $plugin_file ) ) {
+					continue;
+				}
+
+				// Check if the input matches the plugin file in various ways
+				// This mirrors the logic in WP_CLI\Fetchers\Plugin::get()
+				if (
+					( ! empty( $input_name ) && "$input_name.php" === $plugin_file ) ||
+					( ! empty( $input_name ) && $plugin_file === $input_name ) ||
+					( ! empty( $input_name ) && dirname( $plugin_file ) === $input_name && '.' !== $input_name )
+				) {
+					$found_in_active = $plugin_file;
+					break;
+				}
+			}
+
+			if ( $found_in_active ) {
+				// Plugin is in active_plugins but file doesn't exist
+				// Use validate_plugin to confirm the file is missing
+				$validation = validate_plugin( $found_in_active );
+				if ( is_wp_error( $validation ) ) {
+					WP_CLI::warning( "Plugin '{$input_name}' is marked as active but the plugin file does not exist." );
+				}
+			}
+
 			WP_CLI::halt( 1 );
 		}