Add extra instructions regarding how to edit travis.yml.twig file.

.travis.yml

 # do not edit this file manually, instead run the generate:travis-yml console command
-# if you are a Piwik core developer, edit this template file to auto generate the travis.yml: https://github.com/piwik/piwik/blob/master/plugins/CoreConsole/templates/travis.yml.twig
+# if you are a Piwik core developer, edit this template file to auto generate the .travis.yml: https://github.com/piwik/piwik/blob/master/plugins/CoreConsole/templates/travis.yml.twig
+
+# when modifying this file, please consider whether your changes should apply to plugin .travis.yml files. if not, check whether the pluginName twig var is empty,
+# otherwise your changes will be synced with every plugin that uses an auto generated .travis.yml
+
+# also please test generation before committing by running ./console generate:travis-yml --core and ./console generate:travis-yml --plugin=CustomAlerts
+# and making sure the .travis.yml files are changed correctly
 
 language: php
 

plugins/CoreConsole/templates/travis.yml.twig

 # do not edit this file manually, instead run the generate:travis-yml console command
-# if you are a Piwik core developer, edit this template file to auto generate the travis.yml: https://github.com/piwik/piwik/blob/master/plugins/CoreConsole/templates/travis.yml.twig
+{% if pluginName is empty %}
+# if you are a Piwik core developer, edit this template file to auto generate the .travis.yml: https://github.com/piwik/piwik/blob/master/plugins/CoreConsole/templates/travis.yml.twig
+
+# when modifying this file, please consider whether your changes should apply to plugin .travis.yml files. if not, check whether the pluginName twig var is empty,
+# otherwise your changes will be synced with every plugin that uses an auto generated .travis.yml
+
+# also please test generation before committing by running ./console generate:travis-yml --core and ./console generate:travis-yml --plugin=CustomAlerts
+# and making sure the .travis.yml files are changed correctly
+{% endif %}
 
 language: php