Update expected output of passing regression-new tests

[ehildenb]

Part of: https://github.com/runtimeverification/k/issues/4194

This PR adjusts the regression-new/ tests to enable more on CI.

• Expected output is updated:
  • Ones which were previously outputting #Top from kprove and are now outputting PASSED from pyk prove.
  • Ones which were previously omitting generated cells in output from krun are not including them in pyk run.
• The skip list regression-new/skipped is updated with the now-passing tests.
• The testing harness in ktest.mak is updated to reflect better the K testing harness (and run all appropriate tests).
• Many paths in the makefile system are updated to reflect the current setup better.