You only mention once application, so hard to answer this question, but in the example of JIRA connecting to Confluence the incoming authentication to JIRA would allow confluence to create a JIRA issue through confluence, and allow confluence pages to show JIRA issue macro. Other features riding on this configuration is activity streams, linking and what not.
The documentation on the subject is however weak. Today we are supposed to not use basic access, or application trust but simply Oauth with 2 leg authentication (without impersonation) if i understand it correctly.
Thanks @Jonas Andersson.
I have integerated JIRA with non atlassion application.If i create a issue in my tool it will be updated in JIRA using rest api.
If i add comment from my application same comment is added in JIRA also.using incoming authentication in application links configuration.
Now my doubt is if i add a comment to same issue in JIRA side it should be updated in my application.
So how to make a call to my application from JIRA side.
I am not sure i can answer that. While creating an issue from your application you would only use the outgoing link to make sure that user has rights to create an issue on Jira. If you want JIRA to authenticate against your app for some reason i assume you would have to create a plugin in JIRA that interacts and verifies rights in the outgoing direction, but once more this is far beyond my knowledge. I would assume that you started by creating an addon that adds a tab or widget on the JIRA side, and have a REST API interface towards your app, but this is all guessing. Maybe someone else here can answer you better.
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