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When I am starting to build a site that is going to require both HTML and PHP, should I be making a .html file with PHP in it (as in the file would be, say, index.html but within it there would be various tags)? Or, should I be making the files .php files and simply include HTML within it (as in the file would be, again say, index.php and it would start as PHP and I would simply intertwine HTML)?
TL;DR: Should I be weaving HTML into .php files or weaving PHP into .html files?
It should be a PHP file with HTML “weaved” into it. By default if your server sees an HTML file it does not think it needs to process scripts on the page and will render it. If it sees a PHP extension, it knows it needs to run through the PHP Processor.
You can modify your htaccess to allow HTML to be rendered through the processor, but there really is no need for you to be modding that, especially if you are a beginner.