I have just started, on numerous recommendations, to use Zend Studio for PHP development, with Apache as my web server. This works, but only just. Would it perhaps be better to create a super-workspace/project that includes the entire WordPress? Are there any other options? Any Zend plugins that help?
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Zend is closely to no related to WordPress.
You're better off creating a custom local domain + server + apache + bla. Then run a normal WordPress install in it. You should also use the "WordPress Reset"-Plugin to bring (in case) your install back to plain vanilla/as delivered.