In the migrations directory, you will notice that the filenames are prefixed with a number; that is, you will find 1_initial_migration.js and 2_deploy_contracts.js files. The numbered prefix is required in order to record whether the migration ran successfully.

The Migrations contract stores (in last_completed_migration) a number that corresponds to the last applied migration script found in the migrations folder. The Migrations contract is always deployed first. The numbering convention is x_script_name.js, with x starting at 1. Your app contracts would typically come in scripts starting at 2.

So, as this Migrations contract stores the number of the last deployment script applied, truffle will not run these scripts again. On the other hand, in future, your app may need to have a modified, or new, contract deployed. For that to happen, you create a new script with an increased number that describes the steps that need to take place. Then, again, after they have run once, they will not run again.