Move from Joomla to custom site - php

I got thrown this task because no one in my company understands websites, but I have only worked with very basic sites before, so I need help please. I haven't found another question quite like this one.
My company has an established site, running on Joomla 2.5, hosted on GoDaddy. They recently commissioned a company to build them a new site (not Joomla based), but want me to put it up on GoDaddy (saves money). The design company sent me a zip file, and GoDaddy told me to just move all the current site folders into one single folder, then unzip the site in the Public folder.
This is what I'm seeing in cPanel.
And this is what I see in FileZilla.
Do they really mean for me to move ALL these files to one folder? Or are there some I shouldn't touch, like the public_ftp folder? Or only move the files in the Public_html subfolder? Or only move files that are not in any folder?
Please be descriptive, I'm very new. Thanks in advance.

Joomla directories names are very intuitive. For most of them, you can guess the folder content just seeing it name. Basically we have these folders:
Any folder or file does not belong to joomla and therefore you should not move to the new subdirectory.
No changes are required in the database, so that all continue working on www.domain.com/oldweb
root: this is the directory where you made your Joomla pack extraction. When you first place Joomla on your web site, the root directory contains an index.php file that will run the Joomla installer. Once installed Joomla, this index.php page will detect your settings in the configuration.php file and execute your main Joomla engine.
administrator: In this directory you find all files for your Joomla administrator web interface (components, templates, modules, plugins, etc). The Administrator interface itself is a Joomla web site, and has a complete user interface that can be augmented by administrative extensions.
cache: This folder holds Joomla cache files. To accelerate performance, Joomla will cache popular pages requested in this directory, so they don’t have to be re-downloaded by PHP and MySQL for each time it is requested.
components: This directory holds all Joomla components, accept those for your administrator interface. By default, Joomla has some components available, such as login, newsfeeds, poll, registration, search, and others. They are ready to go, and can already displayed them in your website front-end.
images: This folder by default holds images used for your extensions. It contains all bitmaps used by the administrator interface as well as images that have been uploaded to present with article content. Within it you find the \smiles folder that contains emoticons; the \stories folder that has images; and the \banners folder that holds some sample banner files.
includes: In this directory you find core files of Joomla. It contains PHP execution files that automate inclusion of content.
installation: This folder contains needed files for Joomla installation. It should be deleted after installed Joomla.
language: This folder holds all language files. Joomla stores translations in a simple INI-based file format. All languages files are contained in it own folder and have filename prefix that matches the folder name. For example, all language files for English template from the country Great Britain are stored in a folder named eng-GB and all of them has a prefix eng-GB.
libraries: this directory holds your entire Joomla system and third-party libraries used in your website. A Joomla website uses the core libraries contained inside the \libraries folder. Within this folder you find the \joomla folder where you will see different implementations areas (such as file system, application, database, etc). These implementations make up the functional parts of your application. Its library has its own subfolder in this folder to aid in organization.
logs: Where Joomla stores its log files.
media: Default folder to store media files. It may contains files related with user interfaces, such as: JavaScript libraries, flash files, etc.
modules: This folder contains all installed front-end modules. It holds the modules available for display by a template. By default Joomla comes some modules, such as banners, breadcrumbs, latest news, login, newsflash, poll, random image, others. Modules are placed like panels into a Joomla template. They often encapsulate or provide the front-end display for related component. Like a component, a module is a type of add-on extension.
plugins: It contains all your plugins files. As well as components and modules, plugins are a type of add-on extension. However, they work at a lower level than components.
templates: This directory has all your frontend template files. You can notice that the name of each template subfolder must match the template it contains. By default Joomla brings some templates already done, and ready for use.
tmp: This folder stores temporary files and cookies that are used by the administrator and user interface of Joomla. Most of time, extensions’ files are copied to this folder during Joomla installation process.

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I wonder if Wordpress uses any type of configurational inheritance from main site to the nested site

With Wordpress I had only some experience in setting up different sort of plugins, never dealt with how it's done on system and engineering level. Now I'm going to move my site from host to another host and need some advise over the following thing:
with my existing hosting I host 2 web sites: root one (andrtsa.com) and one I created later (oksana.photography) that I noticed is shown with its own content under [public_html]. I do not need old root site, it's outdated, I only want to migrate new one in subfolder. I wonder If I can just take (copy) whatever I have in root folder of my site (folders like [public_ftp], [perl5], [.cpanel] etc), and I'm removing everything from public_html except [oksana.photography] folder which whole content I copy to its parent [public_html] folder like on the picture:
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How to configure Laravel project structure in IntelliJ IDEA?

Which folders I'm supposed to mark as Sources/Resources/Excluded?
My own logic based on the PHPStorm guide
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The root folder
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alternative: Just mark the real folder you have your code inside app, bootstrap, config, routes, (more...)
Click this button to mark the selected folder as the root for
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Appointing a Sources folder is not mandatory but this helps you keep
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See Configuring PHP Namespaces in a Project for details.
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tests
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Excluded
vendor, storage, node_modules
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In storage live caching files, files that have no significant meaning to us, we do not track them in version control (like vendor). We could just delete them and the application would still work. Same for node_modules, but this directory is for javascript packages.
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public
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Can somebody explain in brief the use of assets folder in yii framework. I am new to yii framework
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When a project has multiple versions (production, testing, development, etc.) do not copy the assets/ folders from one area to another; allow Yii to deploy them automatically in each area.
Do not manually edit any file under assets/ - if you have a real need to make a change, find the publishing module, edit the source, delete the subfolder under assets/, and let Yii re-publish the updated files.
Do not reference names under the assets/ folder directly (say, to get at some other module's assets). If you need to use that
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Additional info
Yii makes assets accessible by Web clients, so the goal of copying assets to a Web-accessible directory is fulfilled and returns the corresponding URL for accessing them.
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I am developing a Joomla Component which will allow visitors to download a sound file (be it mp3, or wave, does not matter). Those files are managed in the admin interface and can be unpublished in there.
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Are there any conventions on the placement of those files inside my component's directory structure?
My first idea is to create a folder inside the administrator/components/com_mycomponent and keep the files there. Do I need to restrict access to this new folder with a new .htaccess file, or is it already taken care of by Joomla with a global .htaccess?
you should place the files in the media directory. It is supported by the installer and is much better place. The logic is to have code in com_mycomponent for site and admin and both of those will share media (images/css/js), downloads, etc...
/media/com_mycomponent/
Restrictions are up to you.
Here is Joomla installation structure, http://docs.joomla.org/Components:xml_installfile

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