Q:

best practice when working with a MySQL database datadir directory

At the place I currently work they do some thing I consider strange in the way they work with the MySQL datadir. The directory in which the files that actually store the data are kept. 

$ grep datadir /etc/mysql/my.cnf
  datadir = /var/lib/mysql

Where all the .frm .myd .myi files are found.
When moving data around on the network or doing client installs they copy these files directly out of the this directory and past them into which ever directory they have set up MySQL to use on the client side. They do the same thing at the office. 
I was taught as a Database Administrator that you should work with the scripts. Export the data and structure of the database as a SQL script and import it as a SQL script when you want to start working with it. This is to protect the data integrity. As those files can be in a state inconstant with a working copy of the data. As caches may not have been written to the database files on the disk. I see that they stop the MySQL server when doing the copying and pasting so that should prevent the data becoming corrupt.
I was wandering what industry best practice is around this issue. It seams strange to me. Considering how they view security, concerning passwords and root access I think they have developed a bad practice and are doing it ignorantly. They don't have a strong understanding of some of the fundamentals of how database systems should work. Am I wrong, should I just go with the flow and not get involved with trying to change these practices. 

A:

Generally you will use the proper backup mechanism, mysqldump in the case of MySQL, along with testing that the backup can be successfully restored. It's better to pretend that every backup and restore is being audited by someone very official looking.

