Update nokogiri due to security vulnerability

[lukoktonos]

Nokogiri update for security vulnerability Mongo version added to gemspec so it doesnt update too much.

Other updates occurred after changing gemspec and running bundle install.

Submitter:

• [x] This pull request describes why these changes were made.
• [x] This PR is into the correct branch.
• [x] Internal ticket for this PR: https://jira.mitre.org/browse/BONNIE-1613
• [x] Internal ticket links back to this PR
• [x] Code diff has been done and been reviewed (it does not contain: additional white space, not applicable code changes, debug statements, etc.)
• [x] Tests are included and test edge cases NA
• [x] Tests have been run locally and pass (also ran and passed on staging server)

• [x] Code coverage has not gone down and all code touched or added is covered. NA

  Bonnie Reviewer:

Name: @hossenlopp

• [x] Gemspec/Gemfile updates sanity check