Core

Did just some debugging and found out that $fileObject->deleted is set to TRUE. But the change isn't persisted.

The following 2 changes fixes this.

In \TYPO3\CMS\Core\Resource\ResourceStorage::deleteFile() add:

        // Mark the file object as deleted
        $fileObject->setDeleted();
        $this->updateFile($fileObject);

and change \TYPO3\CMS\Core\Resource\ResourceStorage::updateFile() to:

    protected function updateFile(AbstractFile $file, $identifier = '', $storage = NULL) {
        if ($identifier === '') {
            $identifier = $file->getIdentifier();
        }
        if($file->isDeleted()) {
            $newProperties = array('deleted' => 1);
        } else {
            $fileInfo = $this->driver->getFileInfoByIdentifier($identifier);
            // TODO extend mapping
            $newProperties = array(
                'storage' => $fileInfo['storage'],
                'identifier' => $fileInfo['identifier'],
                'tstamp' => $fileInfo['mtime'],
                'crdate' => $fileInfo['ctime'],
                'mime_type' => $fileInfo['mimetype'],
                'size' => $fileInfo['size'],
                'name' => $fileInfo['name']
            );
        }
        if ($storage !== NULL) {
            $newProperties['storage'] = $storage->getUid();
        }
        $file->updateProperties($newProperties);
        $this->getFileRepository()->update($file);
    }

The last change isn't that nice. would be better the driver returns info about the fact the file is deleted/missing. But at the moment the driver throws an excpetion. Maybe a try...chatch and in the catch set to $newProperties to deleted?

Or only

In \TYPO3\CMS\Core\Resource\ResourceStorage::deleteFile() add:

        // Mark the file object as deleted
        $fileObject->setDeleted();
        $fileObject->updateProperties(array('deleted' => 1));
        $this->getFileRepository()->update($fileObject);

Patch set 2 for branch master has been pushed to the review server.
It is available at https://review.typo3.org/20982

Patch set 3 for branch master has been pushed to the review server.
It is available at https://review.typo3.org/20982

Patch set 1 for branch TYPO3_6-1 has been pushed to the review server.
It is available at https://review.typo3.org/22024

Patch set 1 for branch TYPO3_6-0 has been pushed to the review server.
It is available at https://review.typo3.org/22025

Patch set 1 for branch TYPO3_6-1 has been pushed to the review server.
It is available at https://review.typo3.org/22037

Patch set 1 for branch TYPO3_6-0 has been pushed to the review server.
It is available at https://review.typo3.org/22038

Patch set 1 for branch TYPO3_6-1 has been pushed to the review server.
It is available at https://review.typo3.org/22060

Reverted in all branches due to regressions!

Yes this issue is obsolete now.