This commit adds automation ID to the overlay-base database cache key so
that we properly distinguish different analyses in the same repo for the
same language.
Since I am changing the cache key format, I also moved the CodeQL bundle
version to the end of the cache restore key, in case we want to remove
it from the restore key sometime in the future.
Note that I chose to leave CACHE_VERSION unchanged because the old and
the new cache keys are sufficiently different that there should be no
risk of confusion.
This commit changes overlay database creation to use the
--overlay-changes flag. It also implements Git-based file change
detection to generate the list of files to extract for the overlay
database.
This commit adds a OverlayDatabaseMode parameter to
databaseInitCluster(). The parameter controls the "codeql database init"
flags concerning overlay database creation.
There is no behavior change in this commit because we always pass
OverlayDatabaseMode.None to databaseInitCluster(). That will change in
the next commit.
