Collect known locations from old and new signature.json as well

src/Command/ExecuteCoreUpgradeScriptsCommand.php

@@ -123,11 +123,21 @@ protected function execute(InputInterface $input, OutputInterface $output){
 				return 1;
 			}
 
-			foreach ($locator->getRootDirContent() as $dir){
+			$rootDirContent = array_unique(
+				array_merge(
+					$locator->getRootDirContent(),
+					$locator->getRootDirItemsFromSignature($oldSourcesDir),
+					$locator->getRootDirItemsFromSignature($newSourcesDir)
+				)
+			);
+			foreach ($rootDirContent as $dir){
+				if ($dir === 'updater') {
+					continue;
+				}
 				$this->getApplication()->getLogger()->debug('Replacing ' . $dir);
 				$fsHelper->tripleMove($oldSourcesDir, $newSourcesDir, $tmpDir, $dir);
 			}
-			
+
 			$fsHelper->copyr($tmpDir . '/config/config.php', $oldSourcesDir . '/config/config.php');
 
 			//Get a new shipped apps list
@@ -145,7 +155,7 @@ protected function execute(InputInterface $input, OutputInterface $output){
 				$output->writeln('Copying the application ' . $appId);
 				$fsHelper->copyr($newAppsDir . '/' . $appId, $locator->getOwnCloudRootPath() . '/apps/' . $appId, false);
 			}
-			
+
 			try {
 				$plain = $this->occRunner->run('upgrade');
 				$output->writeln($plain);
@@ -189,20 +199,20 @@ protected function loadVersion($pathToPackage){
 	 */
 	protected function loadAllowedPreviousVersions($pathToPackage) {
 		$canBeUpgradedFrom = $this->loadCanBeUpgradedFrom($pathToPackage);
-		
+
 		$firstItem = reset($canBeUpgradedFrom);
 		if (!is_array($firstItem)){
 			$canBeUpgradedFrom = [$canBeUpgradedFrom];
 		}
-		
+
 		$allowedVersions = [];
 		foreach ($canBeUpgradedFrom as $version){
 			$allowedVersions[] = implode('.', $version);
 		}
 
 		return $allowedVersions;
 	}
-	
+
 	/**
 	 * @param string $pathToPackage
 	 * @return array

src/Utils/Locator.php

@@ -32,7 +32,7 @@ class Locator {
 
 	/**
 	 * absolute path to ownCloud root
-	 * @var string 
+	 * @var string
 	 */
 	protected $ownCloudRootPath;
 
@@ -106,6 +106,7 @@ public function getUpdaterContent(){
 			'box.json',
 			'composer.json',
 			'composer.lock',
+			'CHANGELOG.md',
 			'CONTRIBUTING.md',
 			'COPYING-AGPL',
 			'index.php',
@@ -119,6 +120,27 @@ public function getUpdaterContent(){
 		];
 	}
 
+	/**
+	 * Get all files and directories in the OC root dir using signature.json as a source
+	 *
+	 * @param string $basePath
+	 *
+	 * @return array
+	 */
+	public function getRootDirItemsFromSignature($basePath) {
+		$signature = $this->getSignature($basePath);
+		$items = [];
+		if (isset($signature['hashes'])) {
+			$allItems = array_keys($signature['hashes']);
+			foreach ($allItems as $k => $v) {
+				// Get the part of the string before the first slash or entire string if there is no slash
+				$allItems[$k] = strtok($v, '/');
+			}
+			$items = array_unique($allItems);
+		}
+		return $items;
+	}
+
 	/**
 	 * Absolute path to core root dir content
 	 * @return array
@@ -264,4 +286,20 @@ public function getPathToVersionFile(){
 		return $this->ownCloudRootPath . '/version.php';
 	}
 
+	/**
+	 * @param string $rootPath
+	 *
+	 * @return array|mixed
+	 */
+	private function getSignature($rootPath) {
+		$signature = [];
+		$signaturePath = $rootPath . '/core/signature.json';
+		if (is_file($signaturePath)) {
+			$signature = \json_decode(file_get_contents($signaturePath), true);
+			if (!is_array($signature)) {
+				$signature = [];
+			}
+		}
+		return $signature;
+	}
 }