docs: fix FDE source control assumptions

[namastex888]

Summary

• remove unnecessary npm registry flags from the FDE CLI quickstart; npmjs is the default
• remove GitHub auth as a prerequisite for private app installs
• use private KHAL Gitea placeholders for app repo install/deploy examples
• clarify GitHub exceptions: public docs, app-kit, and desktop due to Mintlify/cloud/SaaS integrations
• update clone/source-control docs to point FDE app work at Gitea

Verification

• python3 -m json.tool docs.json
• git diff --check
• custom docs.json/internal-link checker
• npx -y mint@latest broken-links