Cartridge - Clean up manifests

* Add missing elements or remove unused elements
Change 1 - Consolidate config options into the config file except for --auth
Enable mongodb journaling
Made scripts executable.
Merge pull request #3312 from sridharn/mongodb_journal

Merged by openshift-bot
Fix order of upgrade script in cartridge author doc
Merge pull request #3313 from jwhonce/wip/manifest_lint

Merged by openshift-bot
Merge pull request #3314 from pmorie/docfix

Merged by openshift-bot