My core Comment module is gone
If the comment module files are there in /modules/comment but not displayed in Admin > Modules it suggests the folder isn't readable by the webserver user.

Check the permissions are correct on the /modules/comment folder to allow read access.

For example:

# Run from Drupal root
# Comment module folder ensure readable
chmod 755 modules/comment
# Recursive chmod on files to ensure readable
find modules/comment -type f -exec chmod 644 {} \;