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Now that Conditional Fields 1.0 is out, we can focus on new features for the next version.
The most common problem with CF is compatibility with non-core CCK modules.
Many patches have been proposed to fix issues with single modules (like Date and Content Taxonomy), but I think that we can't simply add them to the main module, because it would become in brief bloated and unmaintainable.
The best long term solution is to add a plug-in system to CF, so every widget has its own conditional settings that allow it to work. To do this, we need to identify the things that conditional fields needs to know to guarantee compatibility.
My ideas are still not clear on the subject, so contributions – also theoretical – are very welcome.