1. Plugins
Backup plugins tend to abuse the resources on servers, so many hosts actually ban them. Those that do not are using CloudLinux, so your plugin will then only slow down your site (or sites, if using ill-advised cPanel addon domains).
So yes, the plugins always make your site run slower.
Honestly, backups should be initiating off-server, not on-server. That way the resources are used on the remote backup server not the web server. Many clients do it on-server, and many control panels and plugins give backup options -- bit it's not ideal. The server and/or the account takes the hit. The larger the backup, the worse it gets. One of our secondary VPS takes a on-server snapshot each night at 2 a.m., and it effectively takes the server offline for 2-5 minutes due to high resource use. Since it's only a secondary server, not serving website content, we just deal with it right now. I'll have to address it later in the year.
A better method would be to use SQLyog ($99) on your local Windows computer, and have it take a nightly scheduled database backup. It makes phpMyAdmin look like a toy by comparison. Processing is all local, and it grab the db backup quickly. We have a Windows VPS specifically for this purpose, and have several backup tasks staggered for hours.
Most users do not pay any attention to this, and just do whatever they want. They just live with the consequences, whatever those may be -- corrupt backups from plugins, the host suspending the site for abuse, slow and/or offline sites while the backup is ongoing.
Of all the WordPress plugins that exist, I'm aware of two of them pretty well.
- WPTwin is not great, and I've seen it cause huge resource spike on servers.
- BackupBuddy from iThemes, however, does not cause a noticeable issue. Of the plugins, I'd begrudgingly try this one first.
2. Why Files?
WordPress backup files are for (1) upload content like images, (2) themes, (3) plugins, (4) any other code or content created outside those standard 3 upload location. Yes, that can be edited core files.
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