If I create a new issue link type (ie. Blocks, Clones, Duplicates, etc...) is there automatic code that runs behind it? How does Block actually stop someone from closing a "Blocked" Issue?
There is nothing in the linking functionality like that. You might as well call "block", "fred" or "kitteh" - it's a label that does nothing.
The exception is "clone", but that's not a function of links really - you can tell Jira "when cloning, link back to the original issue using a link type called X". Once created, the link back to the source issue is no different from block, fred, or kitteh.
However, you can use links in code. The most useful one is a "condition" - they live in the workflow and are there to impose logical conditions on transitions. The off-the-shelf ones are things like "only allow transition if the current user is in group X" or "allow if user is assignee" and so on. But with a spot of code, you can add conditions like "only allow if all issues linked as blockers are resolved" to the resolve transition. There's no such condition in the default app, but there's several in the plugin library. This one for example; https://plugins.atlassian.com/plugins/workflow-toolbox has loads of conditions...
The link for the above plugin is now https://marketplace.atlassian.com/plugins/com.fca.jira.plugins.workflowToolbox.workflow-toolbox.
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