Convert to StandardDex in fixup_dex_dex_file

In fixup_dex_file, run dexlayout to convert compact dex back to
standard dex since the output is supposed to be standard dex.

Fixed a bug in dexlayout where conversion from compact dex ->
standard dex was not supported becuase the dex header was always
preserved.

Test: test/testrunner/testrunner.py  --host ---redefine-stress --compact-dex-level fast
Bug: 63756964

Change-Id: Id13e8593458213e7040d053c35e8914404ae5381