I have enabled Magento 2 Flat table, but how can I rebuild the table manually after add new product’s attributes

You need to run “reindex” command

php bin/magento indexer:reindex

I would like to know if there is any way can create a Magento 2’s store programmatically.

You can call ‘StoreFactory’ class to create Magento 2’s website and use the store resource model to save the store object. Here is the example to create a Magento 2’s store programmatically

$storeFactory = \Magento\Framework\App\ObjectManager::getInstance()
            ->get('Magento\Store\Model\StoreFactory');
$storeResourceModel = \Magento\Framework\App\ObjectManager::getInstance()
            ->get('use Magento\Store\Model\ResourceModel\Store');
$websiteFactory = \Magento\Framework\App\ObjectManager::getInstance()
            ->get('Magento\Store\Model\WebsiteFactory');

$eventManager = \Magento\Framework\App\ObjectManager::getInstance()
            ->get('Magento\Framework\Event\ManagerInterface');


$website = $websiteFactory->create();
$website->load('your_website');
$groupid = 1;

$store= $storeFactory->create();
$store->setCode('new_store');
$store->setName('New Store');
$store->setWebsite($website);
$store->setGroupId($groupid);
$store->setData('is_active','1');
$storeResourceModel->save($store);

$eventManager->dispatch('store_add', ['store' => $store]);

How can I create Magento 2’s website programmatically, like from my custom Magento 2 extension

You can call ‘websiteFactory’ class to create Magento 2’s website and use the website resource model to save the website object. Here is the example to create a Magento 2’s website programmatically

$websiteFactory = \Magento\Framework\App\ObjectManager::getInstance()
            ->get('Magento\Store\Model\WebsiteFactory');
$websiteResourceModel = \Magento\Framework\App\ObjectManager::getInstance()
            ->get('use Magento\Store\Model\ResourceModel\Website');
$website = $websiteFactory->create();

$website->setCode('custom_code');
$website->setName('Custom Name');
$website->setDefaultGroupId(1);
$websiteResourceModel->save($website);

I have created Magento 2 product programmatically, but how can I add or assign new products to exist Magento 2 categories

You will need to get Magento 2 product SKU and category ID first and call assignProductToCategories method from categoryLinkManagement class to assigning the products to exist Magento 2 categories

Here is the example

$sku = "test";
$cids = array(1,2,3);
$link = \Magento\Framework\App\ObjectManager::getInstance()
            ->get('Magento\Catalog\Api\CategoryLinkManagementInterface');
$link->assignProductToCategories($sku,$cids);