Organize VDM flags better

 - Move the deprecated namespace flags to flags/ and make it clear that
   this should not be modified
 - Split the new namespace flags to launched and non-launched for easier
   tracking

#codehealth

Bug: 379646558
Test: presubmit
Flag: EXEMPT no-op cleanup

Change-Id: Ib8dd6b110d9a7fb821b34b4beb2ca49679882664