How to setup Bootstrapping in a project

Sorry if this may have been asked here already, I did search and did not find much.
I am somewhat new to PhpStorm. Switching IDE's and attempting to setup the first project.

Lets say that a portion of the structure is as follows, and is based at DocRoot: 
├── app │   
├── API │   
├── admin │   
├── assets │   
├── client │   
├── grids │   
├── includes │   
├── library │   
├── libs │   
├── logs │   
├── membership │   
├── reports │  
 └── utils 

/app : contains the sites application. 
We have a php index.php in the /app/client directory. 
That index file will "require_once" the /app/bootstrap.inc.php file.  
bootstrap.inc.php will include all the required includes, autoload classes, instantiate required classes, setup a database singleton ($db), etc. 

In PhpStorm, how do I get this to work in the IDE. Site files are on a local drive. 
I have the includes setup to include the /app/includes /app/libs /app/library.
Still have items show up as unresolved in the IDE.. Ex.. $Db is a singleton that was created in the bootstrap.inc.php.

I have this in my bootstrap.inc.php
---------------------

/** @var MySingletonClass $db */
$db = db_driver\Db::instance('app_1');
---------------------

An example use in a file, shows “Undefined  varialbe ‘$db’”

---------------------
<?php
require_once( $_SERVER['DOCUMENT_ROOT'] . '/app/bootstrap.inc.php');
$tRow = $db->query( "SELECT * FROM system_text WHERE st_id=5" )->fetchAll()->results;
---------------------
Even tried a simple php in the same directory as the bootstrap.inc.php

---------------------
<?php
//require_once( $_SERVER['DOCUMENT_ROOT'] . '/app/bootstrap.inc.php');
require_once( 'bootstrap.inc.php');
$tRow = $db->query( "SELECT * FROM system_text WHERE st_id=5" )->fetchAll()->results;
---------------------
Remote site is a remote almalinux lamp stack. Database is a mariadb located on the remote server.

Thanks!!