Is there any way to execute a migration in my Phalcon Application ? and not use the devtools ?
Yes, just load proper classes from devtools in your application and execute migration.
A little help ?
Add devtools to composer.json. Composer update, and load with phalcon loader whole this directory i guess - https://github.com/phalcon/phalcon-devtools/tree/master/scripts/Phalcon not sure which exactly is needed only.