It seemed to me it is kind of a momery problem . 4GB of ram was not enough for the java.exe s trying to compile and run the Jira enviroment (several plugins can not complete to run ).
I simply unistalled 64 bit Java SDK and RTE and installed 32 bit ones . Everything works fine now .
I get exactly the same error - atlas-run starts OK, but localhost:2990/jira returns 404.
My solution is restart JIRA:
Actually I don`t understand the reason of this behaviour, but I hope the double-start helps you.
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