JIRA & Javascript

I have written a Javascript in description and it works well but when i switch between the issue types the javascript doesn't work. What is the effective way to implement Javascripts in Jira . I have 3 environments (Dev, Test, Prod ) and multiple repositories on each environment. I don't feel comforatble customizing the velocity files, which will be overhead task for upgrades.

1. How to implement CSS Changes to custom fields

2. How to implement different presentation of custom fields in different repositories.

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