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I have a PHP/MySQL powered SaaS application which I want to deploy an offline version of. I don't want to use any of the numerous PHP GUI tools that are out there, as this would require rebuilding the GUI and I want it to look exactly the same as the web version.

I want to run Apache/MySQL servers (or something similar) on the clients' systems and somehow compile the PHP code so the source code isn't visible. What is the best way of doing this? Ideally I want to have one .exe file that would start/stop the server.

The following is a very similar question, but it is related to Python and not PHP: Create application for web & desktop

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You can "hide" the source code by creating a compressed phar archive.

As webserver you can use PHP's built in webserver.

As an offline database, normally sqlite is fitting, if you need Mysql, there is an embedded version of Mysql available as well so you can embed that as well, probably through a PHP C extension.

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To take it a step further, package your application with PHP Nightrain. So, you won't have to worry about the user installing PHP, Apache, etc... on his computer. Here's a quick youtube video youtube.com/watch?v=GXt8erPLf4o
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TideSDK would be good option. They provide better support.

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Server2go + Ioncube could be your best o

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There are some tools and technologies that can help in that. Check this list from sitepoint: 3 Ways to Develop Cross Platform Desktop Apps with PHP, and here is an example of application done with PHP: Create your first Desktop Application with PHP and PHP Desktop

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