New in symfony 2.3 the composer install script also copies the parameters.yml.dist file contents into the parameters.yml file, explain
Remove this line twice from your composer.json:
"Incenteev\\ParameterHandler\\ScriptHandler::buildParameters",
This is done by the IncenteevParameterHandler library, which contains a script that does this. By removing the script from the config, it will never be called.
If you remove that line for ever, you can also remove these lines (as the library isn't really needed anymore):
"incenteev/composer-parameter-handler": "~2.0",
...
"incenteev-parameters": {
"file": "app/config/parameters.yml"
},