Having "a clear purpose" means that you know the reason for something. You know why it's happening or why it exists. This phrase is often used in business and in academics.

For example, you might want your company to have a "clear purpose" and for your employees to know what that purpose is:

The difference between a successful business and an unsuccessful one is that successful businesses have a clear purpose.

Things that don't have a clear purpose are unnecessary or unwanted:

If there's no clear purpose to the meeting, then why are we having it?

You can add some other descriptions to "purpose":

Make sure that the project has a clear strategic purpose.