Plugin development without Theme adjustments?

If your code requires themes changes it belongs to the theme, usually the functions.php. In a custom child theme this is not a problem, in a plugin for everyone, it will be much harder. 🙂

The best option to get a theme more flexible: Ask the theme author to add a hook. Provide a real use case. If you don’t want t wait, add the hooks to your child theme. See also ticket #21506 Standard Theme Hooks.

Update
Your use case – changing twentytwelve_entry_meta() – cannot be cross-theme compatible for a simple reason: Not every theme comes with a similar function. Some themes use author name and associated terms in different locations, others don’t show this data at all.

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