The Atlassian plugin SDK is used to create plugins for Atlassian products.
The kit includes two programs, atlas-run and atlas-run-standalone that appear to perform the same task: run some plugins (including yours) within an instance of one of the products.
What is the difference between them?
Found it.
Per this, atlas-run-standalone
Runs an Atlassian application standalone, without a plugin project (that is, not requiring atlas-create--plugin).
...while atlas-run says
Runs the application with your plugin installed. (Runs mvn amps:run.)
which presumably requires a local plugin project.