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3.2 beta will start very soon, final release is generally 2-3 weeks after beta but depends on how large the update is and how many bug fixes there are.

As promised

I think we already did that!

The goal is by the end of next week, but we're cutting it close for that so no guarantees.

As with any custom changes, you will need to merge/update them into any upgrades you perform on your Blesta installation in the future. That's pretty much unavoidable. Even if you use vQmod to avoid editing core files, you'll always have to check that changes to the core don't have adverse affects on your custom changes. vQmod will probably be the best way to integrate your custom changes into core files, assuming you can get it to work properly. Combine that with a custom plugin that registers your new cron task, and you could probably get this to work.

The ability to change which client template to use has been added for v3.2 in CORE-961. You'll always want to keep backups of core template files you modify, and merge them into new releases accordingly. Even if you were using custom templates, you would still need to check them on new releases since data, structure, and language definitions can be added, changed, or removed that has the potential to break things in your templates. The beta releases would be a good time to update your custom templates with these kinds of changes.