Remove cray pointers

[foxtran]

Description
This is a draft PR of removing all cray pointers. I'm splitting it into smaller parts.

This PR can be broken.

Fixes #54

How Has This Been Tested?
Break and fix compilation

Checklist:

• My code follows the style guidelines of this project
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• Any dependent changes have been merged and published in downstream modules
• New check tests, if applicable, are included
• make distcheck passes