Where have the ignore and jira buttons gone on the project page?

If you have followed a link from a commit status you will go to a page for the project which does not include the ignore and create jira issues link. The URL will look something like this: https://app.snyk.io/org/[your org]/test/github/[somestuff]?fromStatus=true&severityThreshold=high
this page is showing you the data on the pull request branch, which is why it doesn't have the jira and ignore functions.

Whereas the https://app.snyk.io/org/[your org]/project/[somestuff] is the project in Snyk and shows the information on your default branch and so therefore has the jira and ignore.