diff --git a/features/check-file-type.feature b/features/check-file-type.feature
index 009801b..7dd4dda 100644
--- a/features/check-file-type.feature
+++ b/features/check-file-type.feature
@@ -1,5 +1,6 @@
 Feature: Check the type of file
 
+  @skip-object-cache @skip-windows
   Scenario: Check that object-cache.php isn't a symlink
     Given a WP install
     And a config.yml file:
@@ -32,7 +33,7 @@ Feature: Check the type of file
       """
     And the return code should be 1
 
-
+  @skip-object-cache @skip-windows
   Scenario: Check that object-cache.php is a symlink
     Given a WP install
     And a config.yml file:
diff --git a/features/check-network-site-option-value.feature b/features/check-network-site-option-value.feature
index d47d907..001c508 100644
--- a/features/check-network-site-option-value.feature
+++ b/features/check-network-site-option-value.feature
@@ -26,7 +26,7 @@ Feature: Check the value of a network option
           option: registration
           value: all
       """
-    And I run `wp eval 'update_site_option( "registration", "none" );'`
+    And I run `wp eval "update_site_option( 'registration', 'none' );"`
 
     When I try `wp doctor check network-registration --config=config.yml`
     Then STDOUT should be a table containing rows:
@@ -38,7 +38,7 @@ Feature: Check the value of a network option
       """
     And the return code should be 1
 
-    When I run `wp eval 'update_site_option( "registration", "all" );'`
+    When I run `wp eval "update_site_option( 'registration', 'all' );"`
     Then STDOUT should be empty
 
     When I run `wp doctor check network-registration --config=config.yml`
@@ -56,7 +56,7 @@ Feature: Check the value of a network option
           option: registration
           value_is_not: none
       """
-    And I run `wp eval 'update_site_option( "registration", "none" );'`
+    And I run `wp eval "update_site_option( 'registration', 'none' );"`
 
     When I try `wp doctor check network-registration --config=config.yml`
     Then STDOUT should be a table containing rows:
@@ -68,7 +68,7 @@ Feature: Check the value of a network option
       """
     And the return code should be 1
 
-    When I run `wp eval 'update_site_option( "registration", "all" );'`
+    When I run `wp eval "update_site_option( 'registration', 'all' );"`
     Then STDOUT should be empty
 
     When I run `wp doctor check network-registration --config=config.yml`
@@ -86,7 +86,7 @@ Feature: Check the value of a network option
           option: registration
           value: none
       """
-    And I run `wp eval 'update_site_option( "registration", array( "users" => "all" ) );'`
+    And I run `wp eval "update_site_option( 'registration', array( 'users' => 'all' ) );"`
 
     When I try `wp doctor check network-registration --config=config.yml`
     Then STDOUT should contain:
diff --git a/features/check.feature b/features/check.feature
index ba4eb00..51b1a14 100644
--- a/features/check.feature
+++ b/features/check.feature
@@ -80,9 +80,9 @@ Feature: Basic check usage
     Then STDOUT should be:
       """
       name,status
-      cache-flush,warning
       option-blog-public,error
       php-in-upload,success
+      cache-flush,warning
       """
     And the return code should be 1
 
@@ -104,8 +104,8 @@ Feature: Basic check usage
     Then STDOUT should be:
       """
       name,status
-      cache-flush,warning
       option-blog-public,error
+      cache-flush,warning
       """
     And the return code should be 1
 
diff --git a/phpstan.neon.dist b/phpstan.neon.dist
new file mode 100644
index 0000000..b753594
--- /dev/null
+++ b/phpstan.neon.dist
@@ -0,0 +1,14 @@
+parameters:
+  level: 9
+  paths:
+    - src
+    - doctor-command.php
+  scanDirectories:
+    - vendor/wp-cli/wp-cli/php
+  scanFiles:
+    - vendor/php-stubs/wordpress-stubs/wordpress-stubs.php
+    - tests/phpstan/scan-files.php
+  treatPhpDocTypesAsCertain: false
+  ignoreErrors:
+    - '#Call to deprecated method setAccessible\(\) of class ReflectionProperty\.#'
+
diff --git a/src/Check.php b/src/Check.php
index c0fc4e2..c86b31b 100644
--- a/src/Check.php
+++ b/src/Check.php
@@ -31,6 +31,8 @@ abstract class Check {
 
 	/**
 	 * Initialize the check.
+	 *
+	 * @param array<string, mixed> $options
 	 */
 	public function __construct( $options = array() ) {
 
@@ -48,6 +50,8 @@ public function __construct( $options = array() ) {
 
 	/**
 	 * Get when the check is expected to run.
+	 *
+	 * @return string
 	 */
 	public function get_when() {
 		return $this->_when;
@@ -57,6 +61,7 @@ public function get_when() {
 	 * Set when the check is expected to run.
 	 *
 	 * @param string $when
+	 * @return void
 	 */
 	public function set_when( $when ) {
 		$this->_when = $when;
@@ -66,6 +71,7 @@ public function set_when( $when ) {
 	 * Set the status of the check.
 	 *
 	 * @param string $status
+	 * @return void
 	 */
 	protected function set_status( $status ) {
 		$this->_status = $status;
@@ -75,6 +81,7 @@ protected function set_status( $status ) {
 	 * Set the message of the check.
 	 *
 	 * @param string $message
+	 * @return void
 	 */
 	protected function set_message( $message ) {
 		$this->_message = $message;
@@ -85,13 +92,15 @@ protected function set_message( $message ) {
 	 *
 	 * Because each check checks for something different, this method must be
 	 * subclassed. Method is expected to set $status_code and $status_message.
+	 *
+	 * @return void
 	 */
 	abstract public function run();
 
 	/**
 	 * Get results of the check.
 	 *
-	 * @return array
+	 * @return array<string, string>
 	 */
 	public function get_results() {
 		return array(
diff --git a/src/Check/Autoload_Options_Size.php b/src/Check/Autoload_Options_Size.php
index db2437d..8752410 100644
--- a/src/Check/Autoload_Options_Size.php
+++ b/src/Check/Autoload_Options_Size.php
@@ -17,6 +17,9 @@ class Autoload_Options_Size extends Check {
 	 */
 	protected $threshold_kb = 900;
 
+	/**
+	 * @return void
+	 */
 	public function run() {
 		ob_start();
 		WP_CLI::run_command(
@@ -40,9 +43,14 @@ public function run() {
 		}
 	}
 
+	/**
+	 * @param int|float $size Size in bytes.
+	 * @param int       $precision Precision.
+	 * @return string
+	 */
 	private static function format_bytes( $size, $precision = 2 ) {
 		$base     = log( $size, 1024 );
 		$suffixes = array( '', 'kb', 'mb', 'g', 't' );
-		return round( pow( 1024, $base - floor( $base ) ), $precision ) . $suffixes[ floor( $base ) ];
+		return round( pow( 1024, $base - floor( $base ) ), $precision ) . $suffixes[ (int) floor( $base ) ];
 	}
 }
diff --git a/src/Check/Cache_Flush.php b/src/Check/Cache_Flush.php
index 3f82d9f..f51e651 100644
--- a/src/Check/Cache_Flush.php
+++ b/src/Check/Cache_Flush.php
@@ -11,6 +11,9 @@
  */
 class Cache_Flush extends File_Contents {
 
+	/**
+	 * @return void
+	 */
 	public function run() {
 
 		// Path to wp-content directory.
@@ -22,6 +25,9 @@ public function run() {
 		$this->regex = 'wp_cache_flush\(\)';
 
 		foreach ( $iterator as $file ) {
+			if ( ! $file instanceof \SplFileInfo ) {
+				continue;
+			}
 			$this->check_file( $file );
 		}
 
@@ -34,7 +40,9 @@ public function run() {
 		// Show relative paths in output.
 		$relative_paths = array_map(
 			function ( $file ) use ( $wp_content_dir ) {
-				return str_replace( $wp_content_dir . '/', '', $file );
+				$normalized_file = \WP_CLI\Path::normalize( (string) $file );
+				$normalized_dir  = \WP_CLI\Path::normalize( $wp_content_dir );
+				return str_replace( rtrim( $normalized_dir, '/' ) . '/', '', $normalized_file );
 			},
 			$this->_matches
 		);
diff --git a/src/Check/Constant_Definition.php b/src/Check/Constant_Definition.php
index 765a6b8..c33cfae 100644
--- a/src/Check/Constant_Definition.php
+++ b/src/Check/Constant_Definition.php
@@ -26,9 +26,9 @@ class Constant_Definition extends Check {
 	/**
 	 * Whether or not the constant is expected to be a falsy value.
 	 *
-	 * @var bool
+	 * @var bool|null
 	 */
-	protected $falsy;
+	protected $falsy = null;
 
 	/**
 	 * Expected value of the constant.
@@ -39,6 +39,8 @@ class Constant_Definition extends Check {
 
 	/**
 	 * Initialize the constant check
+	 *
+	 * @param array<string, mixed> $options
 	 */
 	public function __construct( $options = array() ) {
 		parent::__construct( $options );
@@ -47,6 +49,9 @@ public function __construct( $options = array() ) {
 		}
 	}
 
+	/**
+	 * @return void
+	 */
 	public function run() {
 
 		if ( isset( $this->falsy ) ) {
@@ -99,7 +104,7 @@ public function run() {
 			return;
 		}
 
-		if ( $this->defined && ! isset( $this->value ) ) {
+		if ( ! isset( $this->value ) ) {
 			$this->set_status( 'success' );
 			$this->set_message( "Constant '{$this->constant}' is defined." );
 			return;
@@ -118,12 +123,21 @@ public function run() {
 		}
 	}
 
+	/**
+	 * @param mixed $value
+	 * @return string
+	 */
 	private static function human_value( $value ) {
 		if ( true === $value ) {
-			$value = 'true';
+			return 'true';
 		} elseif ( false === $value ) {
-			$value = 'false';
+			return 'false';
+		} elseif ( is_null( $value ) ) {
+			return 'null';
+		}
+		if ( is_scalar( $value ) ) {
+			return (string) $value;
 		}
-		return $value;
+		return gettype( $value );
 	}
 }
diff --git a/src/Check/Core_Update.php b/src/Check/Core_Update.php
index 55d4c4d..1f2b43e 100644
--- a/src/Check/Core_Update.php
+++ b/src/Check/Core_Update.php
@@ -13,11 +13,17 @@ class Core_Update extends Check {
 	public function run() {
 		ob_start();
 		WP_CLI::run_command( array( 'core', 'check-update' ), array( 'format' => 'json' ) );
-		$ret       = ob_get_clean();
-		$updates   = ! empty( $ret ) ? json_decode( $ret, true ) : array();
+		$ret     = ob_get_clean();
+		$updates = ! empty( $ret ) ? json_decode( $ret, true ) : array();
+		if ( ! is_array( $updates ) ) {
+			$updates = array();
+		}
 		$has_minor = false;
 		$has_major = false;
 		foreach ( $updates as $update ) {
+			if ( ! is_array( $update ) || ! isset( $update['update_type'] ) ) {
+				continue;
+			}
 			switch ( $update['update_type'] ) {
 				case 'minor':
 					$has_minor = true;
diff --git a/src/Check/Core_Verify_Checksums.php b/src/Check/Core_Verify_Checksums.php
index 3b7abdf..300dc50 100644
--- a/src/Check/Core_Verify_Checksums.php
+++ b/src/Check/Core_Verify_Checksums.php
@@ -10,11 +10,17 @@
  */
 class Core_Verify_Checksums extends Check {
 
+	/**
+	 * @param array<string, mixed> $options
+	 */
 	public function __construct( $options = array() ) {
 		parent::__construct( $options );
 		$this->set_when( 'before_wp_load' );
 	}
 
+	/**
+	 * @return void
+	 */
 	public function run() {
 		$return_code = WP_CLI::runcommand(
 			'core verify-checksums',
diff --git a/src/Check/Cron.php b/src/Check/Cron.php
index 3b4e1de..77a9da0 100644
--- a/src/Check/Cron.php
+++ b/src/Check/Cron.php
@@ -7,8 +7,14 @@
 
 abstract class Cron extends Check {
 
+	/**
+	 * @var array<array<string, mixed>>|null
+	 */
 	protected static $crons;
 
+	/**
+	 * @return array<array<string, mixed>>
+	 */
 	protected static function get_crons() {
 
 		if ( isset( self::$crons ) ) {
@@ -23,8 +29,13 @@ protected static function get_crons() {
 				'fields' => 'hook,args',
 			)
 		);
-		$ret         = ob_get_clean();
-		self::$crons = ! empty( $ret ) ? json_decode( $ret, true ) : array();
+		$ret     = ob_get_clean();
+		$decoded = ! empty( $ret ) ? json_decode( $ret, true ) : array();
+		if ( ! is_array( $decoded ) ) {
+			$decoded = array();
+		}
+		/** @var array<array<string, mixed>> $decoded */
+		self::$crons = $decoded;
 		return self::$crons;
 	}
 }
diff --git a/src/Check/Cron_Count.php b/src/Check/Cron_Count.php
index 31cdde9..f9494c6 100644
--- a/src/Check/Cron_Count.php
+++ b/src/Check/Cron_Count.php
@@ -14,6 +14,9 @@ class Cron_Count extends Cron {
 	 */
 	protected $threshold_count = 50;
 
+	/**
+	 * @return void
+	 */
 	public function run() {
 		$crons = self::get_crons();
 		if ( count( $crons ) >= $this->threshold_count ) {
diff --git a/src/Check/Cron_Duplicates.php b/src/Check/Cron_Duplicates.php
index b21eef5..ad4e5fa 100644
--- a/src/Check/Cron_Duplicates.php
+++ b/src/Check/Cron_Duplicates.php
@@ -14,11 +14,17 @@ class Cron_Duplicates extends Cron {
 	 */
 	protected $threshold_count = 10;
 
+	/**
+	 * @return void
+	 */
 	public function run() {
 		$crons             = self::get_crons();
 		$job_counts        = array();
 		$excess_duplicates = false;
 		foreach ( $crons as $job ) {
+			if ( ! isset( $job['hook'] ) ) {
+				continue;
+			}
 			$key_data = array( $job['hook'], isset( $job['args'] ) ? $job['args'] : array() );
 			if ( function_exists( 'wp_json_encode' ) ) {
 				$key = wp_json_encode( $key_data );
diff --git a/src/Check/File.php b/src/Check/File.php
index fc1b496..2d9b95d 100644
--- a/src/Check/File.php
+++ b/src/Check/File.php
@@ -12,7 +12,7 @@ abstract class File extends Check {
 	/**
 	 * File checks are run as their own group.
 	 */
-	protected $_when = false;
+	protected $_when = 'manual'; // Run manually via group
 
 	/**
 	 * File extension to check.
@@ -42,14 +42,14 @@ abstract class File extends Check {
 	/**
 	 * Any files matching the check.
 	 *
-	 * @var array
+	 * @var array<string|\SplFileInfo>
 	 */
 	protected $_matches = array();
 
 	/**
 	 * Get the options for this check
 	 *
-	 * @return string
+	 * @return array<string, bool|string>
 	 */
 	public function get_options() {
 		return array(
@@ -58,4 +58,12 @@ public function get_options() {
 			'path'            => $this->path,
 		);
 	}
+
+	/**
+	 * Check a specific file.
+	 *
+	 * @param \SplFileInfo $file File to check.
+	 * @return void
+	 */
+	abstract public function check_file( \SplFileInfo $file );
 }
diff --git a/src/Check/File_Contents.php b/src/Check/File_Contents.php
index 4927c08..c4431cb 100644
--- a/src/Check/File_Contents.php
+++ b/src/Check/File_Contents.php
@@ -12,9 +12,9 @@ class File_Contents extends File {
 	/**
 	 * Regex pattern to check against each file’s contents.
 	 *
-	 * @var string
+	 * @var string|null
 	 */
-	protected $regex;
+	protected $regex = null;
 
 	/**
 	 * Assert existence or absence of the regex pattern.
@@ -56,12 +56,19 @@ public function run() {
 		}
 	}
 
+	/**
+	 * @param SplFileInfo $file
+	 * @return void
+	 */
 	public function check_file( SplFileInfo $file ) {
 		if ( $file->isDir() || ! isset( $this->regex ) ) {
 			return;
 		}
 
 		$contents = file_get_contents( $file->getPathname() );
+		if ( false === $contents ) {
+			return;
+		}
 
 		if ( preg_match( '#' . $this->regex . '#i', $contents ) ) {
 			$this->_matches[] = $file;
diff --git a/src/Check/File_Type.php b/src/Check/File_Type.php
index 1a161f1..445c3d5 100644
--- a/src/Check/File_Type.php
+++ b/src/Check/File_Type.php
@@ -2,8 +2,6 @@
 
 namespace WP_CLI\Doctor\Check;
 
-use SplFileInfo;
-
 /**
  * Checks files on the filesystem to be of a certain type.
  */
@@ -12,9 +10,9 @@ class File_Type extends File {
 	/**
 	 * Assert the file type is or isn't a symlink.
 	 *
-	 * @var bool
+	 * @var bool|null
 	 */
-	protected $symlink;
+	protected $symlink = null;
 
 	public function run() {
 
@@ -32,7 +30,11 @@ public function run() {
 		}
 	}
 
-	public function check_file( SplFileInfo $file ) {
+	/**
+	 * @param \SplFileInfo $file
+	 * @return void
+	 */
+	public function check_file( \SplFileInfo $file ) {
 		if ( isset( $this->symlink ) ) {
 			if ( 'link' === $file->getType() && false === $this->symlink ) {
 				$this->_matches[] = $file;
diff --git a/src/Check/Language_Update.php b/src/Check/Language_Update.php
index ec12882..c0f19bc 100644
--- a/src/Check/Language_Update.php
+++ b/src/Check/Language_Update.php
@@ -22,6 +22,10 @@ public function run() {
 			)
 		);
 
+		if ( ! is_array( $languages ) ) {
+			$languages = [];
+		}
+
 		// Returns the count of each value that the key 'update' is mapped to.
 		$counts = array_count_values( array_column( $languages, 'update' ) );
 
diff --git a/src/Check/Network_Required_Plugins.php b/src/Check/Network_Required_Plugins.php
index 970bb90..a510bda 100644
--- a/src/Check/Network_Required_Plugins.php
+++ b/src/Check/Network_Required_Plugins.php
@@ -13,10 +13,13 @@ class Network_Required_Plugins extends Check {
 	/**
 	 * List of required plugin slugs.
 	 *
-	 * @var array
+	 * @var array<string>
 	 */
 	protected $plugins = array();
 
+	/**
+	 * @param array<string, mixed> $options
+	 */
 	public function __construct( $options = array() ) {
 		parent::__construct( $options );
 
@@ -32,6 +35,9 @@ public function __construct( $options = array() ) {
 		}
 	}
 
+	/**
+	 * @return void
+	 */
 	public function run() {
 		if ( ! is_multisite() ) {
 			$this->set_status( 'success' );
@@ -80,10 +86,8 @@ public function run() {
 	}
 
 	/**
-	 * Resolve a plugin slug or file to an installed plugin file path.
-	 *
-	 * @param string $plugin_slug Requested plugin slug/file.
-	 * @param array  $installed_plugins Installed plugins keyed by plugin file.
+	 * @param string               $plugin_slug Requested plugin slug/file.
+	 * @param array<string, mixed> $installed_plugins Installed plugins keyed by plugin file.
 	 * @return string|null
 	 */
 	private function get_plugin_file( $plugin_slug, $installed_plugins ) {
diff --git a/src/Check/Network_Site_Count.php b/src/Check/Network_Site_Count.php
index f2359ef..721c498 100644
--- a/src/Check/Network_Site_Count.php
+++ b/src/Check/Network_Site_Count.php
@@ -24,6 +24,9 @@ class Network_Site_Count extends Check {
 	 */
 	protected $maximum = 500;
 
+	/**
+	 * @param array<string, mixed> $options
+	 */
 	public function __construct( $options = array() ) {
 		parent::__construct( $options );
 
@@ -34,6 +37,9 @@ public function __construct( $options = array() ) {
 		}
 	}
 
+	/**
+	 * @return void
+	 */
 	public function run() {
 		if ( ! is_multisite() ) {
 			$this->set_status( 'success' );
diff --git a/src/Check/Network_Site_Option_Value.php b/src/Check/Network_Site_Option_Value.php
index 3b750b7..dfe3d00 100644
--- a/src/Check/Network_Site_Option_Value.php
+++ b/src/Check/Network_Site_Option_Value.php
@@ -30,6 +30,9 @@ class Network_Site_Option_Value extends Check {
 	 */
 	protected $value_is_not;
 
+	/**
+	 * @return void
+	 */
 	public function run() {
 		if ( ! is_multisite() ) {
 			$this->set_status( 'success' );
@@ -95,6 +98,9 @@ private function format_value_for_message( $value ) {
 		if ( false === $value ) {
 			return 'false';
 		}
-		return (string) $value;
+		if ( is_scalar( $value ) ) {
+			return (string) $value;
+		}
+		return gettype( $value );
 	}
 }
diff --git a/src/Check/Option_Value.php b/src/Check/Option_Value.php
index 5122fe5..1735cdc 100644
--- a/src/Check/Option_Value.php
+++ b/src/Check/Option_Value.php
@@ -30,6 +30,9 @@ class Option_Value extends Check {
 	 */
 	protected $value_is_not;
 
+	/**
+	 * @return void
+	 */
 	public function run() {
 
 		if ( isset( $this->value ) && isset( $this->value_is_not ) ) {
@@ -38,24 +41,29 @@ public function run() {
 			return;
 		}
 
+		if ( ! isset( $this->value ) && ! isset( $this->value_is_not ) ) {
+			$this->set_status( 'error' );
+			$this->set_message( 'You must use either "value" or "value_is_not".' );
+			return;
+		}
+
 		$actual_value = get_option( $this->option );
 
 		if ( isset( $this->value ) ) {
 			if ( $actual_value == $this->value ) { // phpcs:ignore Universal.Operators.StrictComparisons -- Keep existing behavior.
 				$status  = 'success';
-				$message = "Option '{$this->option}' is '{$this->value}' as expected.";
+				$message = "Option '{$this->option}' is '" . $this->format_value_for_message( $this->value ) . "' as expected.";
 			} else {
 				$status  = 'error';
-				$message = "Option '{$this->option}' is '{$actual_value}' but expected to be '{$this->value}'.";
-			}
-		} elseif ( isset( $this->value_is_not ) ) {
-			if ( $actual_value == $this->value_is_not ) { // phpcs:ignore Universal.Operators.StrictComparisons -- Keep existing behavior.
-				$status  = 'error';
-				$message = "Option '{$this->option}' is '{$actual_value}' and expected not to be.";
-			} else {
-				$status  = 'success';
-				$message = "Option '{$this->option}' is not '{$this->value_is_not}' as expected.";
+				$message = "Option '{$this->option}' is '" . $this->format_value_for_message( $actual_value ) . "' but expected to be '" . $this->format_value_for_message( $this->value ) . "'.";
 			}
+		} elseif ( $actual_value == $this->value_is_not ) { // phpcs:ignore Universal.Operators.StrictComparisons -- Keep existing behavior.
+			$status  = 'error';
+			$message = "Option '{$this->option}' is '" . $this->format_value_for_message( $actual_value ) . "' and expected not to be.";
+
+		} else {
+			$status  = 'success';
+			$message = "Option '{$this->option}' is not '" . $this->format_value_for_message( $this->value_is_not ) . "' as expected.";
 		}
 
 		$this->set_status( $status );
@@ -78,4 +86,34 @@ public function run() {
 				break;
 		}
 	}
+
+	/**
+	 * Format arbitrary option values for stable string output.
+	 *
+	 * @param mixed $value Value to render.
+	 * @return string
+	 */
+	private function format_value_for_message( $value ) {
+		if ( is_array( $value ) || is_object( $value ) ) {
+			$encoded = wp_json_encode( $value );
+			if ( false !== $encoded ) {
+				return $encoded;
+			}
+			return 'unrepresentable value';
+		}
+
+		if ( null === $value ) {
+			return 'null';
+		}
+		if ( true === $value ) {
+			return 'true';
+		}
+		if ( false === $value ) {
+			return 'false';
+		}
+		if ( is_scalar( $value ) ) {
+			return (string) $value;
+		}
+		return gettype( $value );
+	}
 }
diff --git a/src/Check/PHP_In_Upload.php b/src/Check/PHP_In_Upload.php
index ae257d5..549e7f9 100644
--- a/src/Check/PHP_In_Upload.php
+++ b/src/Check/PHP_In_Upload.php
@@ -14,10 +14,13 @@ class PHP_In_Upload extends Check {
 	/**
 	 * Array containing list of files found in the uploads folder
 	 *
-	 * @var array
+	 * @var array<\SplFileInfo>
 	 */
 	protected $php_files_array = array();
 
+	/**
+	 * @return void
+	 */
 	public function run() {
 
 		// Path to the uploads folder.
@@ -26,6 +29,9 @@ public function run() {
 		$iterator       = new RecursiveIteratorIterator( $directory, RecursiveIteratorIterator::CHILD_FIRST );
 
 		foreach ( $iterator as $file ) {
+			if ( ! $file instanceof \SplFileInfo ) {
+				continue;
+			}
 			if ( 'php' === $file->getExtension() ) {
 				$this->php_files_array[] = $file;
 			}
diff --git a/src/Check/Plugin.php b/src/Check/Plugin.php
index b759be9..ff876b3 100644
--- a/src/Check/Plugin.php
+++ b/src/Check/Plugin.php
@@ -7,8 +7,14 @@
 
 abstract class Plugin extends Check {
 
+	/**
+	 * @var array<array<string, mixed>>|null
+	 */
 	protected static $plugins;
 
+	/**
+	 * @return array<array<string, mixed>>
+	 */
 	protected static function get_plugins() {
 
 		if ( isset( self::$plugins ) ) {
@@ -17,8 +23,13 @@ protected static function get_plugins() {
 
 		ob_start();
 		WP_CLI::run_command( array( 'plugin', 'list' ), array( 'format' => 'json' ) );
-		$ret           = ob_get_clean();
-		self::$plugins = ! empty( $ret ) ? json_decode( $ret, true ) : array();
+		$ret     = ob_get_clean();
+		$decoded = ! empty( $ret ) ? json_decode( $ret, true ) : array();
+		if ( ! is_array( $decoded ) ) {
+			$decoded = array();
+		}
+		/** @var array<array<string, mixed>> $decoded */
+		self::$plugins = $decoded;
 		return self::$plugins;
 	}
 }
diff --git a/src/Check/Plugin_Active_Count.php b/src/Check/Plugin_Active_Count.php
index ea0e7c5..85b7a53 100644
--- a/src/Check/Plugin_Active_Count.php
+++ b/src/Check/Plugin_Active_Count.php
@@ -14,9 +14,15 @@ class Plugin_Active_Count extends Plugin {
 	 */
 	protected $threshold_count = 80;
 
+	/**
+	 * @return void
+	 */
 	public function run() {
 		$active = 0;
 		foreach ( self::get_plugins() as $plugin ) {
+			if ( ! isset( $plugin['status'] ) ) {
+				continue;
+			}
 			if ( 'active' === $plugin['status'] || 'active-network' === $plugin['status'] ) {
 				++$active;
 			}
diff --git a/src/Check/Plugin_Deactivated.php b/src/Check/Plugin_Deactivated.php
index b63c95d..63bf568 100644
--- a/src/Check/Plugin_Deactivated.php
+++ b/src/Check/Plugin_Deactivated.php
@@ -14,12 +14,18 @@ class Plugin_Deactivated extends Plugin {
 	 */
 	protected $threshold_percentage = 40;
 
+	/**
+	 * @return void
+	 */
 	public function run() {
 		$plugins = self::get_plugins();
 
 		$active   = 0;
 		$inactive = 0;
 		foreach ( self::get_plugins() as $plugin ) {
+			if ( ! isset( $plugin['status'] ) ) {
+				continue;
+			}
 			if ( 'active' === $plugin['status'] || 'active-network' === $plugin['status'] ) {
 				++$active;
 			} elseif ( 'inactive' === $plugin['status'] ) {
diff --git a/src/Check/Plugin_Status.php b/src/Check/Plugin_Status.php
index 20e5fe0..f287982 100644
--- a/src/Check/Plugin_Status.php
+++ b/src/Check/Plugin_Status.php
@@ -27,6 +27,9 @@ class Plugin_Status extends Plugin {
 	 */
 	protected $status;
 
+	/**
+	 * @param array<string, mixed> $options
+	 */
 	public function __construct( $options = array() ) {
 		$valid_statuses = array( 'uninstalled', 'installed', 'active' );
 		if ( ! in_array( $options['status'], $valid_statuses, true ) ) {
@@ -35,13 +38,19 @@ public function __construct( $options = array() ) {
 		parent::__construct( $options );
 	}
 
+	/**
+	 * @return void
+	 */
 	public function run() {
 		$plugins = self::get_plugins();
 
 		$current_status = 'uninstalled';
 		foreach ( self::get_plugins() as $plugin ) {
+			if ( ! isset( $plugin['name'] ) || ! isset( $plugin['status'] ) ) {
+				continue;
+			}
 			if ( $plugin['name'] === $this->name ) {
-				$current_status = $plugin['status'];
+				$current_status = is_string( $plugin['status'] ) ? $plugin['status'] : 'uninstalled';
 				break;
 			}
 		}
diff --git a/src/Check/Plugin_Update.php b/src/Check/Plugin_Update.php
index c37a277..7d9bf0d 100644
--- a/src/Check/Plugin_Update.php
+++ b/src/Check/Plugin_Update.php
@@ -7,10 +7,16 @@
  */
 class Plugin_Update extends Plugin {
 
+	/**
+	 * @return void
+	 */
 	public function run() {
 		$plugins      = self::get_plugins();
 		$update_count = 0;
 		foreach ( $plugins as $plugin ) {
+			if ( ! isset( $plugin['update'] ) ) {
+				continue;
+			}
 			if ( 'available' === $plugin['update'] ) {
 				++$update_count;
 			}
diff --git a/src/Check/Theme_Update.php b/src/Check/Theme_Update.php
index dd3a679..ddc6654 100644
--- a/src/Check/Theme_Update.php
+++ b/src/Check/Theme_Update.php
@@ -10,13 +10,22 @@
  */
 class Theme_Update extends Check {
 
+	/**
+	 * @return void
+	 */
 	public function run() {
 		ob_start();
 		WP_CLI::run_command( array( 'theme', 'list' ), array( 'format' => 'json' ) );
-		$ret          = ob_get_clean();
-		$themes       = ! empty( $ret ) ? json_decode( $ret, true ) : array();
+		$ret    = ob_get_clean();
+		$themes = ! empty( $ret ) ? json_decode( $ret, true ) : array();
+		if ( ! is_array( $themes ) ) {
+			$themes = array();
+		}
 		$update_count = 0;
 		foreach ( $themes as $theme ) {
+			if ( ! is_array( $theme ) || ! isset( $theme['update'] ) ) {
+				continue;
+			}
 			if ( 'available' === $theme['update'] ) {
 				++$update_count;
 			}
diff --git a/src/Checks.php b/src/Checks.php
index d13f9b7..07f970a 100644
--- a/src/Checks.php
+++ b/src/Checks.php
@@ -4,15 +4,29 @@
 
 use Mustangostang\Spyc;
 use WP_CLI;
-use WP_CLI\Utils;
+use WP_CLI\Path;
+
 
 class Checks {
 
+	/**
+	 * @var Checks|null
+	 */
 	private static $instance;
 
-	private $checks         = array();
+	/**
+	 * @var array<string, \WP_CLI\Doctor\Check>
+	 */
+	private $checks = array();
+
+	/**
+	 * @var array<string, array<string>>
+	 */
 	private $skipped_checks = array();
 
+	/**
+	 * @return Checks
+	 */
 	public static function get_instance() {
 		if ( ! isset( self::$instance ) ) {
 			self::$instance = new Checks();
@@ -24,13 +38,19 @@ public static function get_instance() {
 	 * Register checks from a config file
 	 *
 	 * @param string $file
+	 * @return void
 	 */
 	public static function register_config( $file ) {
 		if ( ! is_file( $file ) ) {
 			WP_CLI::error( 'Invalid configuration file.' );
 		}
 
-		$check_data = Spyc::YAMLLoad( file_get_contents( $file ) );
+		$contents = file_get_contents( $file );
+		if ( false === $contents ) {
+			WP_CLI::error( 'Could not read configuration file.' );
+		}
+
+		$check_data = Spyc::YAMLLoad( $contents );
 
 		if ( ! empty( $check_data['_']['inherit'] ) ) {
 			$inherited = $check_data['_']['inherit'];
@@ -77,8 +97,9 @@ public static function register_config( $file ) {
 	/**
 	 * Register a check with the Doctor
 	 *
-	 * @param string $name Name for the check.
-	 * @param string $class Check class name.
+	 * @param string        $name  Name for the check.
+	 * @param object|string $check Check class name or instance.
+	 * @return void
 	 */
 	public static function add_check( $name, $check ) {
 
@@ -96,21 +117,25 @@ public static function add_check( $name, $check ) {
 			$class = get_class( $check );
 			WP_CLI::error( "Class '{$class}' for check '{$name}' needs to extend Check base class. Verify check registration." );
 		}
-		self::$instance->checks[ $name ] = $check;
+		self::get_instance()->checks[ $name ] = $check;
 	}
 
 	/**
-	 * Get checks registred with the Doctor.
+	 * Get checks registered with the Doctor.
 	 *
-	 * @param array $args Filter checks based on some attribute.
+	 * @param array<string, mixed> $args Filter checks based on some attribute.
+	 * @return array<string, \WP_CLI\Doctor\Check>
 	 */
 	public static function get_checks( $args = array() ) {
 		if ( ! empty( $args['name'] ) ) {
 			$checks = array();
 			$names  = is_array( $args['name'] ) ? $args['name'] : array( $args['name'] );
 			foreach ( $names as $name ) {
-				if ( isset( self::$instance->checks[ $name ] ) ) {
-					$checks[ $name ] = self::$instance->checks[ $name ];
+				if ( ! is_string( $name ) ) {
+					continue;
+				}
+				if ( isset( self::get_instance()->checks[ $name ] ) ) {
+					$checks[ $name ] = self::get_instance()->checks[ $name ];
 				}
 			}
 			return $checks;
@@ -123,9 +148,10 @@ public static function get_checks( $args = array() ) {
 	 *
 	 * @param string $path Path to file.
 	 * @param string $base Base path to prepend.
+	 * @return string
 	 */
 	private static function absolutize( $path, $base ) {
-		if ( ! empty( $path ) && ! Utils\is_path_absolute( $path ) ) {
+		if ( ! empty( $path ) && ! Path::is_absolute( $path ) ) {
 			$path = $base . DIRECTORY_SEPARATOR . $path;
 		}
 		return $path;
diff --git a/src/Command.php b/src/Command.php
index 2f6d6db..3dd5753 100644
--- a/src/Command.php
+++ b/src/Command.php
@@ -108,10 +108,13 @@ class Command {
 	 *     +--------------------+--------+--------------------------------------------+
 	 *
 	 * @when before_wp_load
+	 *
+	 * @param array<string>        $args       Names of one or more checks to run.
+	 * @param array<string, bool|string> $assoc_args Command options.
+	 * @return void
 	 */
 	public function check( $args, $assoc_args ) {
-
-		$config = Utils\get_flag_value( $assoc_args, 'config', self::get_default_config() );
+		$config = (string) Utils\get_flag_value( $assoc_args, 'config', self::get_default_config() );
 		Checks::register_config( $config );
 
 		$all = Utils\get_flag_value( $assoc_args, 'all' );
@@ -135,7 +138,7 @@ public function check( $args, $assoc_args ) {
 		}
 		foreach ( $checks as $name => $check ) {
 			$when = $check->get_when();
-			if ( $when ) {
+			if ( $when && 'manual' !== $when ) {
 				WP_CLI::add_hook(
 					$when,
 					static function () use ( $name, $check, &$completed, &$progress ) {
@@ -156,56 +159,6 @@ static function () use ( $name, $check, &$completed, &$progress ) {
 				}
 			}
 		}
-		if ( ! empty( $file_checks ) ) {
-			WP_CLI::add_hook(
-				'after_wp_config_load',
-				static function () use ( $file_checks, &$completed, &$progress ) {
-					WP_CLI::debug( 'Scanning filesystem for file checks...', 'doctor' );
-					try {
-						$directory      = new RecursiveDirectoryIterator( ABSPATH, RecursiveDirectoryIterator::SKIP_DOTS );
-						$iterator       = new RecursiveIteratorIterator( $directory, RecursiveIteratorIterator::CHILD_FIRST );
-						$wp_content_dir = defined( 'WP_CONTENT_DIR' ) ? WP_CONTENT_DIR : ABSPATH . 'wp-content';
-						$item_count     = 0;
-						foreach ( $iterator as $file ) {
-							++$item_count;
-							if ( 0 === $item_count % self::DEBUG_FILE_SCAN_INTERVAL ) {
-								WP_CLI::debug( "  Visited {$item_count} items...", 'doctor' );
-							}
-							foreach ( $file_checks as $name => $check ) {
-								$options = $check->get_options();
-								if ( ! empty( $options['only_wp_content'] )
-								&& 0 !== stripos( $file->getPath(), $wp_content_dir ) ) {
-									continue;
-								}
-								if ( ! empty( $options['path'] )
-								&& 0 !== stripos( $file->getPathname(), ABSPATH . $options['path'] ) ) {
-									continue;
-								}
-								$extension = explode( '|', $options['extension'] );
-								if ( ! in_array( $file->getExtension(), $extension, true ) ) {
-									continue;
-								}
-								$check->check_file( $file );
-							}
-						}
-						WP_CLI::debug( "  Total items visited: {$item_count}", 'doctor' );
-					} catch ( Exception $e ) {
-						WP_CLI::warning( $e->getMessage() );
-					}
-					foreach ( $file_checks as $name => $check ) {
-						WP_CLI::debug( "Running check: {$name}", 'doctor' );
-						$check->run();
-						$completed[ $name ] = $check;
-						if ( $progress ) {
-							$progress->tick();
-						}
-						$results = $check->get_results();
-						WP_CLI::debug( "  Status: {$results['status']}", 'doctor' );
-					}
-				}
-			);
-		}
-
 		if ( ! isset( WP_CLI::get_runner()->config['url'] ) ) {
 			WP_CLI::add_wp_hook(
 				'muplugins_loaded',
@@ -221,6 +174,52 @@ static function () {
 			WP_CLI::warning( $e->getMessage() );
 		}
 
+		// Run file checks manually after WordPress is loaded.
+		if ( ! empty( $file_checks ) ) {
+			WP_CLI::debug( 'Scanning filesystem for file checks...', 'doctor' );
+			try {
+				$directory      = new RecursiveDirectoryIterator( ABSPATH, RecursiveDirectoryIterator::SKIP_DOTS );
+				$iterator       = new RecursiveIteratorIterator( $directory, RecursiveIteratorIterator::CHILD_FIRST );
+				$wp_content_dir = defined( 'WP_CONTENT_DIR' ) ? WP_CONTENT_DIR : ABSPATH . 'wp-content';
+				foreach ( $iterator as $file ) {
+					if ( ! $file instanceof \SplFileInfo ) {
+						continue;
+					}
+					foreach ( $file_checks as $name => $check ) {
+						$options = $check->get_options();
+						if ( ! empty( $options['only_wp_content'] )
+						&& 0 !== stripos( \WP_CLI\Path::normalize( $file->getPath() ), \WP_CLI\Path::normalize( $wp_content_dir ) ) ) {
+							continue;
+						}
+						if ( ! empty( $options['path'] )
+						&& 0 !== stripos( \WP_CLI\Path::normalize( $file->getPathname() ), \WP_CLI\Path::normalize( ABSPATH . $options['path'] ) ) ) {
+							continue;
+						}
+
+						$ext_option = isset( $options['extension'] ) && is_string( $options['extension'] ) ? $options['extension'] : '';
+						$extension  = explode( '|', $ext_option );
+						if ( ! in_array( $file->getExtension(), $extension, true ) ) {
+							continue;
+						}
+						/** @var Check\File $check */
+						$check->check_file( $file );
+					}
+				}
+			} catch ( Exception $e ) {
+				WP_CLI::warning( $e->getMessage() );
+			}
+			foreach ( $file_checks as $name => $check ) {
+				WP_CLI::debug( "Running check: {$name}", 'doctor' );
+				$check->run();
+				$completed[ $name ] = $check;
+				if ( $progress ) {
+					$progress->tick();
+				}
+				$results = $check->get_results();
+				WP_CLI::debug( "  Status: {$results['status']}", 'doctor' );
+			}
+		}
+
 		$results = array();
 		foreach ( $completed as $name => $check ) {
 			$results[] = array_merge( $check->get_results(), array( 'name' => $name ) );
@@ -332,6 +331,10 @@ function ( $check ) {
 	 *
 	 * @when before_wp_load
 	 * @subcommand list
+	 *
+	 * @param array<string>        $args       Command arguments.
+	 * @param array<string, bool|string> $assoc_args Command options.
+	 * @return void
 	 */
 	public function list_( $args, $assoc_args ) {
 
@@ -342,13 +345,14 @@ public function list_( $args, $assoc_args ) {
 			$assoc_args
 		);
 
-		$config = Utils\get_flag_value( $assoc_args, 'config', self::get_default_config() );
+		$config = (string) Utils\get_flag_value( $assoc_args, 'config', self::get_default_config() );
 		Checks::register_config( $config );
 
 		$items = array();
 		foreach ( Checks::get_checks() as $check_name => $class ) {
 			$reflection  = new \ReflectionClass( $class );
-			$description = self::remove_decorations( $reflection->getDocComment() );
+			$doc_comment = $reflection->getDocComment();
+			$description = $doc_comment ? self::remove_decorations( $doc_comment ) : '';
 			$tokens      = array();
 			foreach ( $reflection->getProperties() as $prop ) {
 				$prop_name = $prop->getName();
@@ -362,7 +366,11 @@ public function list_( $args, $assoc_args ) {
 				if ( is_array( $value ) ) {
 					$value = json_encode( $value );
 				}
-				$tokens[ '%' . $prop_name . '%' ] = $value;
+				if ( is_scalar( $value ) ) {
+					$tokens[ '%' . $prop_name . '%' ] = (string) $value;
+				} else {
+					$tokens[ '%' . $prop_name . '%' ] = gettype( $value );
+				}
 			}
 			if ( ! empty( $tokens ) ) {
 				$description = str_replace( array_keys( $tokens ), array_values( $tokens ), $description );
@@ -373,11 +381,13 @@ public function list_( $args, $assoc_args ) {
 				'description' => $description,
 			);
 		}
-		Utils\format_items( $assoc_args['format'], $items, explode( ',', $assoc_args['fields'] ) );
+		Utils\format_items( (string) $assoc_args['format'], $items, explode( ',', (string) $assoc_args['fields'] ) );
 	}
 
 	/**
 	 * Runs through the entirety of the WP bootstrap process
+	 *
+	 * @return void
 	 */
 	private function load_wordpress_with_template() {
 		global $wp_query;
@@ -437,14 +447,22 @@ static function ( $template ) {
 	 * @return string
 	 */
 	private static function remove_decorations( $comment ) {
-		$comment = preg_replace( '|^/\*\*[\r\n]+|', '', $comment );
-		$comment = preg_replace( '|\n[\t ]*\*/$|', '', $comment );
-		$comment = preg_replace( '|^[\t ]*\* ?|m', '', $comment );
+		$replaced = preg_replace( '|^/\*\*[\r\n]+|', '', $comment );
+		$comment  = is_string( $replaced ) ? $replaced : '';
+
+		$replaced = preg_replace( '|\n[\t ]*\*/$|', '', $comment );
+		$comment  = is_string( $replaced ) ? $replaced : '';
+
+		$replaced = preg_replace( '|^[\t ]*\* ?|m', '', $comment );
+		$comment  = is_string( $replaced ) ? $replaced : '';
+
 		return $comment;
 	}
 
 	/**
 	 * Get the path to the default config file
+	 *
+	 * @return string
 	 */
 	private static function get_default_config() {
 		return dirname( __DIR__ ) . '/doctor.yml';
diff --git a/tests/phpstan/scan-files.php b/tests/phpstan/scan-files.php
new file mode 100644
index 0000000..81f3d91
--- /dev/null
+++ b/tests/phpstan/scan-files.php
@@ -0,0 +1,6 @@
+<?php
+// phpcs:ignoreFile
+
+namespace {
+	define( 'WPINC', 'wp-includes' );
+}