What's the difference between xdebug.ini and php.ini
Ubuntu is based on Debian. Debian and it's derivatives use a somewhat unique way of managing extensions for php and apache.
Of the files you have listed:
/etc/php/7.0/apache2/conf.d/20-xdebug.ini is a symlink to /etc/php/7.0/mods-available/xdebug.ini
/etc/php/7.0/cli/conf.d/20-xdebug.ini is also a symlink to /etc/php/7.0/mods-available/xdebug.ini
- You can edit /etc/php/7.0/mods-available/xdebug.ini directly and changes you make will affect everywhere it is enabled.
Commands phpenmod and phpdismod are available to enable or disable PHP modules. These are like a2enmod for apache, which you can read about here. For example, turn XDebug off with sudo phpdismod xdebug. Turn it back on with sudo phpenmod xdebug. Your configuration will be preserved when you flip it on and off because your changes are always preserved in mods-available, although PHP does not look in that directory for configuration. In fact, when you "disable" the module with phpdismod, it's simply removing the symlink from the appropriate folder so that the module is not enabled in the php config.
Finally, /etc/php/7.0/apache2/php.ini is the location for system-wide config that is not a module that can be enabled or disabled.
Thus, your config changes like xdebug.remote_port = 9000 should go in /etc/php/7.0/mods-available/xdebug.ini since it's related to XDebug. Putting it in both places is a bad idea (because of the confusion it creates), but the last one to load takes precedence. This is why many of the files in the mods-available directory have numbers in the filename - so they'll load in the correct order.
Use the phpinfo() function to get more info about which config values were loaded and what ini files they were loaded from. For example:
$ php -r "phpinfo();"
or
$ php -r "phpinfo();" | grep xdebug
This depends on how PHP was compiled. Take a look at how PHP was compiled by reviewing the list of .ini files it is loading and from where they are being loaded.
From the command line, type the following and review:
$ php -i | grep .ini
Or, you can learn of this by creating a temporary PHP file and visiting it in a browser. Just be sure to name it something difficult to find, and delete it right after you're done; e.g., /info-949w30.php. Why? Because this report may leak full filesystem paths, version numbers, and other details.
<?php phpinfo();
PHP has two directives that are established when it's compiled.
--with-config-file-path=path/to/main.ini--with-config-file-scan-dir=/scan/this/dir/for/other.inifiles.
The main .ini file is loaded first, and then files in the scan-dir are loaded alphabetically after that. Which is why you see a lot of .ini files using a numeric prefix. That's an easy way to take control over the load order. Changing the name of the file in relation to others in the directory.