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.
