Fix API communication

Summary:
Fix API communication between Confluence and other Atlassian products.
Add a new config (bypass.APIs) to enable application links.
Fix the unprotected.dirs config to not overwrite default values.
Update amps and plugin versions.

Test Plan: Tested with local Confluence and Jira instances. Made sure API comunication works with Duo installed on both ends.

Reviewers: boyangz, peter

Subscribers: dev

Differential Revision: https://phab.duosec.org/D5482