Well, I like and have often seen a shady moss bed with native ephemerals sprinkled through it.

Clover on the other hand usually doesn't grow in shade. So, if correctly identified, this must be a sunny area ?

If it is a sunny area in particular, you will find things popping up with much more frequency (imo).

the front yard is partial shade and the yard has moss and clover.

Irismead, can you add a photo of the clover? Different types may or may not create issues as far as competing with natives, depending on what the natives are, the particular clover type, and how much light there is. The moss won't be an issue as far as competition, I don't think.

Where are you? What is native varies a lot depending on where you are in the country. Most of the spring ephemerals are shade lovers, at least in the northeastern part of the US. There are plenty of sun-loving natives which are more likely to be around all season in my area.

Are you planning on only perennials, or shrubs, vines or trees as well? You may want to mulch to prevent new weeds from sprouting while you are waiting for plants to fill in.