Addressed PR comments.

Applied Heidi's comments

Addressed Harshula's comments + minor other fixes:
- Specified Spack **managed** environments when necessary
- Fix output bad formatting in virtual terminals
- Changed reference to $(prefix) to point out $spack instead
- Changed part for the output formatting to refer to the specific Spack instance installed throught the setup
- Changed a 'data="input"' line to 'data="output"' for the virtual terminal related to "spack find mom5"

Addressed Harshula and Anton's comments

Added Harshula's suggestions.