From d2a9ab711015bbfcec53ca08469f2275c67dfeb1 Mon Sep 17 00:00:00 2001
From: Joao Silva <geral@joaocsilva.com>
Date: Wed, 1 Mar 2023 09:09:07 +0100
Subject: [PATCH 1/6] DQA-0: Test config.

---
 tests/fixtures/commands/configuration.yml | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/tests/fixtures/commands/configuration.yml b/tests/fixtures/commands/configuration.yml
index b461b9278..311a8f1a2 100644
--- a/tests/fixtures/commands/configuration.yml
+++ b/tests/fixtures/commands/configuration.yml
@@ -318,3 +318,19 @@
   expectations:
     - string_contains: "root: build"
     - string_contains: "base_url: 'http://web:8080'"
+
+- command: 'config action'
+  configuration: []
+  resources:
+    - file: runner.yml.dist
+      content: |
+        color: red
+        action: 'Color is ${color}'
+    - file: runner.yml
+      content: |
+        color: yellow
+    - file: config/runner/colors.yml
+      content: |
+        color: blue
+  expectations:
+    - string_contains: "Color is yellow"

From f1b64becd79ff8d8bda77935f6ffcd80c8683629 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=2E=20Jo=C3=A3o=20Santos?= <jonhy81@gmail.com>
Date: Wed, 1 Mar 2023 09:56:29 +0100
Subject: [PATCH 2/6] Update configuration.yml

---
 tests/fixtures/commands/configuration.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tests/fixtures/commands/configuration.yml b/tests/fixtures/commands/configuration.yml
index 311a8f1a2..7cc492e3d 100644
--- a/tests/fixtures/commands/configuration.yml
+++ b/tests/fixtures/commands/configuration.yml
@@ -329,8 +329,10 @@
     - file: runner.yml
       content: |
         color: yellow
+        action: 'Color is ${color}'
     - file: config/runner/colors.yml
       content: |
         color: blue
+        action: 'Color is ${color}'
   expectations:
     - string_contains: "Color is yellow"

From 845f7c6f288e8720ed3053bd10918f885a280658 Mon Sep 17 00:00:00 2001
From: Joao Silva <geral@joaocsilva.com>
Date: Wed, 1 Mar 2023 20:08:12 +0100
Subject: [PATCH 3/6] Revert "Update configuration.yml"

This reverts commit f1b64becd79ff8d8bda77935f6ffcd80c8683629.
---
 tests/fixtures/commands/configuration.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tests/fixtures/commands/configuration.yml b/tests/fixtures/commands/configuration.yml
index 7cc492e3d..311a8f1a2 100644
--- a/tests/fixtures/commands/configuration.yml
+++ b/tests/fixtures/commands/configuration.yml
@@ -329,10 +329,8 @@
     - file: runner.yml
       content: |
         color: yellow
-        action: 'Color is ${color}'
     - file: config/runner/colors.yml
       content: |
         color: blue
-        action: 'Color is ${color}'
   expectations:
     - string_contains: "Color is yellow"

From b0032cc9b2a6314f7f4b85c262747400cb747b74 Mon Sep 17 00:00:00 2001
From: Joao Silva <geral@joaocsilva.com>
Date: Thu, 2 Mar 2023 09:13:40 +0100
Subject: [PATCH 4/6] DQA-0: Refactor Runner prepare config.

---
 config/base.yml                           |   3 -
 config/default.yml                        |   2 +
 src/TaskRunner/Runner.php                 | 156 +++++++++-------------
 tests/fixtures/commands/configuration.yml |  26 ++++
 4 files changed, 91 insertions(+), 96 deletions(-)

diff --git a/config/base.yml b/config/base.yml
index 067cfb18c..e69de29bb 100644
--- a/config/base.yml
+++ b/config/base.yml
@@ -1,3 +0,0 @@
-runner:
-  bin_dir: './vendor/bin'
-  bin_node_dir: './node_modules/.bin'
diff --git a/config/default.yml b/config/default.yml
index 80d25b222..e971af757 100644
--- a/config/default.yml
+++ b/config/default.yml
@@ -1,6 +1,8 @@
 runner:
   bin_dir: './vendor/bin'
   bin_node_dir: './node_modules/.bin'
+  # This property cannot contain a reference to a variable as it will
+  # not be processed before the load of configurations in given directory.
   config_dir: './config/runner'
 symlink_project:
   ignore: [ '.idea', 'vendor' ]
diff --git a/src/TaskRunner/Runner.php b/src/TaskRunner/Runner.php
index f3ebd9930..458cfbb7f 100644
--- a/src/TaskRunner/Runner.php
+++ b/src/TaskRunner/Runner.php
@@ -5,12 +5,11 @@
 namespace EcEuropa\Toolkit\TaskRunner;
 
 use Composer\Autoload\ClassLoader;
-use Consolidation\Config\ConfigInterface;
-use Consolidation\Config\Loader\ConfigProcessor;
-use Consolidation\Config\Util\ConfigOverlay;
+use Dflydev\DotAccessData\Data;
 use EcEuropa\Toolkit\TaskRunner\Commands\ConfigurationCommands;
 use EcEuropa\Toolkit\TaskRunner\Inject\ConfigForCommand;
 use EcEuropa\Toolkit\Toolkit;
+use Grasmash\Expander\Expander;
 use League\Container\Container;
 use Psr\Container\ContainerInterface;
 use Robo\Application;
@@ -22,6 +21,7 @@
 use Symfony\Component\Console\Input\InputInterface;
 use Symfony\Component\Console\Input\InputOption;
 use Symfony\Component\Console\Output\OutputInterface;
+use Symfony\Component\Yaml\Yaml;
 
 /**
  * Toolkit Runner.
@@ -90,7 +90,7 @@ class Runner
      *
      * @var string[]
      */
-    private $overrides = [
+    private array $overrides = [
         'toolkit.build.dist.keep',
         'toolkit.test.phpcs.standards',
         'toolkit.test.phpcs.ignore_patterns',
@@ -198,6 +198,26 @@ private function prepareApplication()
         return $this;
     }
 
+    /**
+     * Recursively merge config files.
+     *
+     * @param array $files
+     *   The file paths to fetch the configs.
+     * @param array|null $config
+     *   The given, the new configs will be merged.
+     */
+    private function parseConfigFiles(array $files, array $config = null): array
+    {
+        $config = $config ?? [];
+        foreach ($files as $file) {
+            $content = Yaml::parseFile($file);
+            if (!empty($content) && is_array($content)) {
+                $config = array_replace_recursive($config, $content);
+            }
+        }
+        return $config;
+    }
+
     /**
      * Create the configurations and process overrides.
      *
@@ -206,41 +226,50 @@ private function prepareApplication()
     private function prepareConfigurations()
     {
         $workingDir = realpath($this->workingDir);
-        // Load Toolkit default configuration.
-        $defaultConfig = Robo::createConfiguration([Toolkit::getToolkitRoot() . '/config/default.yml']);
-        $defaultConfig->set('runner.working_dir', $workingDir);
-        $this->loadConfigurationFromDirFiles($defaultConfig);
-
-        // Re-build configuration.
-        $context = $defaultConfig->getContext(ConfigOverlay::DEFAULT_CONTEXT);
-
-        $processor = new ConfigProcessor();
-        $processor->add($defaultConfig->export());
-
-        $currentConfig = $this->getCurrentConfig($workingDir, $defaultConfig);
-        if (isset($currentConfig)) {
-            // Allow some configurations to be overridden. If a given property is
-            // defined on a project level it will replace the default values
-            // instead of merge.
-            foreach ($this->overrides as $override) {
-                if ($value = $currentConfig->get($override)) {
-                    $context->set($override, $value);
-                }
-            }
+        // Load the Toolkit default configurations.
+        $config = $this->parseConfigFiles([Toolkit::getToolkitRoot() . '/config/default.yml']);
+        $config['runner']['working_dir'] = $workingDir;
+        $tkConfigDir = Toolkit::getToolkitRoot() . '/' . $config['runner']['config_dir'];
+        $files = $this->getConfigDirFilesPaths($tkConfigDir);
+        $config = $this->parseConfigFiles($files, $config);
+
+        // Save the project configurations separately to allow the overrides.
+        $projectConfig = [];
+        // Load the Project configuration.
+        if (file_exists($workingDir . '/runner.yml.dist')) {
+            $projectConfig = $this->parseConfigFiles([$workingDir . '/runner.yml.dist']);
+        }
 
-            $processor->add($currentConfig->export());
+        // Check if the project has dynamic configs.
+        $projectConfigDir = $workingDir . '/' . ($projectConfig['runner']['config_dir'] ?? $config['runner']['config_dir']);
+        if ($tkConfigDir !== $projectConfigDir) {
+            if (!empty($files = $this->getConfigDirFilesPaths($projectConfigDir))) {
+                $projectConfig = $this->parseConfigFiles($files, $projectConfig);
+            }
         }
 
-        // Allow runner.yml to override configurations. Is recommended to keep
-        // this out of VCS control to allow local config customizations.
+        // Usually the runner.yml is used for local development and is not committed
+        // to the repo, load it as last so it can override values properly.
         if (file_exists($workingDir . '/runner.yml')) {
-            $configOverride = new Config();
-            Robo::loadConfiguration([$workingDir . '/runner.yml'], $configOverride);
-            $processor->add($configOverride->export());
+            $projectConfig = $this->parseConfigFiles([$workingDir . '/runner.yml'], $projectConfig);
         }
 
-        // Import newly built configuration.
-        $this->config->replace($processor->export());
+        // Merge the toolkit and project configurations.
+        $config = array_replace_recursive($config, $projectConfig);
+
+        $expander = new Expander();
+        $result = $expander->expandArrayProperties($config);
+        $this->config->replace($result);
+
+        // Allow some configurations to be overridden. If a given property is
+        // defined on a project level it will replace the default values
+        // instead of merge.
+        $projectConfigLoaded = new Data($projectConfig);
+        foreach ($this->overrides as $override) {
+            if ($value = $projectConfigLoaded->get($override, null)) {
+                $this->config->set($override, $value);
+            }
+        }
 
         return $this;
     }
@@ -344,37 +373,6 @@ private function registerConfigurationCommands()
         }
     }
 
-    /**
-     * Get current configurations.
-     *
-     * @param string $workingDir
-     * @param ConfigInterface $defaultConfig
-     *
-     * @return ConfigInterface|null
-     */
-    private function getCurrentConfig(string $workingDir, ConfigInterface $defaultConfig): ?ConfigInterface
-    {
-        $configFile = '';
-        if (file_exists($workingDir . '/runner.yml.dist')) {
-            $configFile = $workingDir . '/runner.yml.dist';
-        }
-
-        $defaultConfigDir = $defaultConfig->get(self::CONFIG_DIR_KEY);
-        $configDirFilesPaths = $this->getConfigDirFilesPaths((string) realpath($defaultConfigDir));
-        if (empty($configFile) && empty($configDirFilesPaths)) {
-            return null;
-        }
-
-        if (!empty($configFile)) {
-            $currentConfig = Robo::createConfiguration([realpath($configFile)]);
-            $this->loadConfigurationFromDirFiles($currentConfig, false, $defaultConfigDir);
-
-            return $currentConfig;
-        }
-
-        return Robo::createConfiguration($configDirFilesPaths);
-    }
-
     /**
      * Get runner config directory files.
      *
@@ -384,35 +382,7 @@ private function getCurrentConfig(string $workingDir, ConfigInterface $defaultCo
      */
     private function getConfigDirFilesPaths(string $runnerConfigDir): array
     {
-        return glob($runnerConfigDir . '/*.yml');
-    }
-
-    /**
-     * Load configuration from dir files.
-     *
-     * @param ConfigInterface $config
-     * @param bool $isToolkitRoot
-     * @param string|null $fallbackConfigDir
-     *
-     * @return void
-     */
-    private function loadConfigurationFromDirFiles(ConfigInterface $config, bool $isToolkitRoot = true, ?string $fallbackConfigDir = null): void
-    {
-        $configDir = $config->get(self::CONFIG_DIR_KEY, $fallbackConfigDir);
-        if (empty($configDir)) {
-            return;
-        }
-
-        $configDir = $isToolkitRoot
-            ? Toolkit::getToolkitRoot() . '/' . $configDir
-            : realpath($configDir);
-
-        $configFilesPaths = $this->getConfigDirFilesPaths((string) $configDir);
-        if (empty($configFilesPaths)) {
-            return;
-        }
-
-        Robo::loadConfiguration($configFilesPaths, $config);
+        return glob($runnerConfigDir . '/*.yml') ?? [];
     }
 
 }
diff --git a/tests/fixtures/commands/configuration.yml b/tests/fixtures/commands/configuration.yml
index 311a8f1a2..90507e25e 100644
--- a/tests/fixtures/commands/configuration.yml
+++ b/tests/fixtures/commands/configuration.yml
@@ -334,3 +334,29 @@
         color: blue
   expectations:
     - string_contains: "Color is yellow"
+
+- command: 'config toolkit.test.phpcs.files'
+  configuration: []
+  resources: []
+  expectations:
+    - contains: |
+        - ./lib
+        - ./resources
+        - ./src
+
+- command: 'config toolkit.test.phpcs.files'
+  configuration: []
+  resources:
+    - file: runner.yml.dist
+      content: |
+        toolkit:
+          test:
+            phpcs:
+              files:
+                - file1
+                - file2
+  expectations:
+    - contains: |
+        - file1
+        - file2
+    - not_string_contains: src

From bc177e410007589937e2846450847dc85fe716b9 Mon Sep 17 00:00:00 2001
From: Joao Silva <geral@joaocsilva.com>
Date: Thu, 2 Mar 2023 09:52:57 +0100
Subject: [PATCH 5/6] DQA-0: Allow hook init to set properties.

---
 src/TaskRunner/Runner.php | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/TaskRunner/Runner.php b/src/TaskRunner/Runner.php
index 458cfbb7f..91cfe9ad3 100644
--- a/src/TaskRunner/Runner.php
+++ b/src/TaskRunner/Runner.php
@@ -135,7 +135,6 @@ public function __construct(ClassLoader $classLoader, InputInterface $input, Out
         // Create application.
         $this
             ->prepareApplication()
-            ->prepareConfigurations()
             ->prepareContainer()
             ->prepareRunner();
     }
@@ -150,6 +149,7 @@ public function run()
     {
         $classes = $this->discoverCommandClasses();
         $this->runner->registerCommandClasses($this->application, $classes);
+        $this->prepareConfigurations();
         $this->registerConfigurationCommands();
         return $this->runner->run($this->input, $this->output, $this->application);
     }
@@ -237,7 +237,7 @@ private function prepareConfigurations()
         $projectConfig = [];
         // Load the Project configuration.
         if (file_exists($workingDir . '/runner.yml.dist')) {
-            $projectConfig = $this->parseConfigFiles([$workingDir . '/runner.yml.dist']);
+            $projectConfig = $this->parseConfigFiles([$workingDir . '/runner.yml.dist'], $projectConfig);
         }
 
         // Check if the project has dynamic configs.

From ee88abb3f9436564eb8641fe2d9f42bc348a8351 Mon Sep 17 00:00:00 2001
From: Joao Silva <geral@joaocsilva.com>
Date: Thu, 2 Mar 2023 16:12:07 +0100
Subject: [PATCH 6/6] DQA-0: Cover command options configs.

---
 resources/git/hooks/pre-commit            |  2 +-
 src/TaskRunner/AbstractCommands.php       | 10 -----
 src/TaskRunner/Runner.php                 | 18 +++++++--
 src/Toolkit.php                           |  4 +-
 tests/fixtures/commands/configuration.yml | 46 +++++++++++++++++++++++
 5 files changed, 64 insertions(+), 16 deletions(-)

diff --git a/resources/git/hooks/pre-commit b/resources/git/hooks/pre-commit
index 6c3421f66..c2d6e636b 100755
--- a/resources/git/hooks/pre-commit
+++ b/resources/git/hooks/pre-commit
@@ -3,7 +3,7 @@
 # Called by "git commit" with no arguments. The hook should exit with non-zero
 # status after issuing an appropriate message if it wants to stop the commit.
 #
-# This hook should execute the PHPcs agaisnt the modified files.
+# This hook should execute the PHPcs against the modified files.
 #
 
 ./vendor/bin/run toolkit:hooks-run `basename "$0"`
diff --git a/src/TaskRunner/AbstractCommands.php b/src/TaskRunner/AbstractCommands.php
index a708e1c49..2cb977b73 100644
--- a/src/TaskRunner/AbstractCommands.php
+++ b/src/TaskRunner/AbstractCommands.php
@@ -32,16 +32,6 @@ public function getConfigurationFile()
         return Toolkit::getToolkitRoot() . '/config/base.yml';
     }
 
-    /**
-     * Command initialization.
-     *
-     * @hook pre-command-event *
-     */
-    public function initializeRuntimeConfiguration()
-    {
-        Robo::loadConfiguration([$this->getConfigurationFile()], $this->getConfig());
-    }
-
     /**
      * Validate and return the path to given bin.
      *
diff --git a/src/TaskRunner/Runner.php b/src/TaskRunner/Runner.php
index 91cfe9ad3..b9cf296b7 100644
--- a/src/TaskRunner/Runner.php
+++ b/src/TaskRunner/Runner.php
@@ -34,7 +34,6 @@ class Runner
 
     public const APPLICATION_NAME = 'Toolkit Runner';
     public const REPOSITORY = 'ec-europa/toolkit';
-    public const CONFIG_DIR_KEY = 'runner.config_dir';
 
     /**
      * The input.
@@ -85,6 +84,13 @@ class Runner
      */
     private $workingDir;
 
+    /**
+     * The loaded command classes.
+     *
+     * @var array
+     */
+    private array $commandClasses;
+
     /**
      * Configurations that can be replaced by a project.
      *
@@ -147,8 +153,8 @@ public function __construct(ClassLoader $classLoader, InputInterface $input, Out
      */
     public function run()
     {
-        $classes = $this->discoverCommandClasses();
-        $this->runner->registerCommandClasses($this->application, $classes);
+        $this->commandClasses = $this->discoverCommandClasses();
+        $this->runner->registerCommandClasses($this->application, $this->commandClasses);
         $this->prepareConfigurations();
         $this->registerConfigurationCommands();
         return $this->runner->run($this->input, $this->output, $this->application);
@@ -233,6 +239,12 @@ private function prepareConfigurations()
         $files = $this->getConfigDirFilesPaths($tkConfigDir);
         $config = $this->parseConfigFiles($files, $config);
 
+        // Get the command options configurations from loaded command classes.
+        foreach ($this->commandClasses as $commandClass) {
+            $f = $this->runner->getContainer()->get("{$commandClass}Commands")->getConfigurationFile() ?? '';
+            $config = $this->parseConfigFiles([$f], $config);
+        }
+
         // Save the project configurations separately to allow the overrides.
         $projectConfig = [];
         // Load the Project configuration.
diff --git a/src/Toolkit.php b/src/Toolkit.php
index fe09ad323..67dcad019 100644
--- a/src/Toolkit.php
+++ b/src/Toolkit.php
@@ -105,9 +105,9 @@ public static function getNextcloudPass(): string
      */
     public static function filterFolders(array &$files)
     {
-        $files = array_filter($files, function ($folder) {
+        $files = array_values(array_filter($files, function ($folder) {
             return file_exists($folder);
-        });
+        }));
     }
 
     /**
diff --git a/tests/fixtures/commands/configuration.yml b/tests/fixtures/commands/configuration.yml
index 90507e25e..25ee0295d 100644
--- a/tests/fixtures/commands/configuration.yml
+++ b/tests/fixtures/commands/configuration.yml
@@ -360,3 +360,49 @@
         - file1
         - file2
     - not_string_contains: src
+
+- command: 'toolkit:test-behat --simulate'
+  configuration: []
+  resources:
+    - file: runner.yml.dist
+      content: |
+        toolkit:
+          test:
+            behat:
+              from: test-behat.yml.dist
+  expectations:
+    - contains: |
+        [Simulator] Simulating Exec('./vendor/bin/run toolkit:install-dependencies')
+        [Simulator] Running ./vendor/bin/run toolkit:install-dependencies
+        [Simulator] Simulating EcEuropa\Toolkit\Task\File\Process('test-behat.yml.dist', 'behat.yml')
+        [Simulator] Running ./vendor/bin/behat --profile=default --strict --dry-run
+        [Simulator] Simulating Exec('./vendor/bin/behat')
+          ->options(array (
+            'profile' => 'default',
+            'strict' => NULL,
+          ), '=')
+        [Simulator] Running ./vendor/bin/behat --profile=default --strict
+
+- command: 'toolkit:test-behat --simulate'
+  configuration: []
+  resources:
+    - touch: test-behat.yml.dist
+    - file: runner.yml.dist
+      content: |
+        command:
+          toolkit:
+            test-behat:
+              options:
+                from: test-behat.yml.dist
+  expectations:
+    - contains: |
+        [Simulator] Simulating Exec('./vendor/bin/run toolkit:install-dependencies')
+        [Simulator] Running ./vendor/bin/run toolkit:install-dependencies
+        [Simulator] Simulating EcEuropa\Toolkit\Task\File\Process('test-behat.yml.dist', 'behat.yml')
+        [Simulator] Running ./vendor/bin/behat --profile=default --strict --dry-run
+        [Simulator] Simulating Exec('./vendor/bin/behat')
+          ->options(array (
+            'profile' => 'default',
+            'strict' => NULL,
+          ), '=')
+        [Simulator] Running ./vendor/bin/behat --profile=default --strict