We at Botron have implemented couple of times HR systems based on JIRA.There isn't one big plug-in, but several smaller ones - for different automation tasks were used.
What features do you want this HR system to have?
Yes, I've supported and improved several places that do this. The tools are flexible and hence should follow your processes, rather than trying to drive it.
One approach, to give you an idea, is to model each person as a JIRA issue, with a workflow that starts maybe with "job offer accepted", and works through the processes of joining and leaving, fields for department and so-on, and links to Confluence for detailed docs - your list of things you're looking for translate well into templates for Confluence docs.
Variable - some were a couple of hundred people, the largest a shade over 10,000.
The admin is moderately simple - JIRA tasks created to remind people to do reviews etc, templates in Confluence to allow quick creation of standardised docs, and so-on. What matters is your process.
Mostly plain JIRA and Confluence. None of the add-ons we used were essential to the systems, but there were some very useful ones. We made use of the script-runner to do things like automatically create "review" sub-tasks regularly, and a blueprint add-on written for creating "department/project spaces" for when they needed a new one set up
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