16.0 Changes: Updates for default flags from deprecated migrations

After the migration work for 16.0, some of the flags will become default (and should be required). Update main.go to require the following arguments or environment vars.

• index_name_commits
• traversal-ids

The integration tests in integration_test.go needs a few updates to support this:

• Update the run method to send the required arguments
• The buildWorkingIndex method does not need to support a separate index for commits so that should be refactored
• The index verification done in TestIndexingCommits, TestIndexingGitlabTest, TestIndexingWikiBlobs, TestSeparateIndexingProjectWikiBlobs should also include checking that the related project permissions and visibility levels are indexed. This is currently only tested in indexer_test.go
• Do not keep any tests that test paths for deprecated migrations (specifically thinking about when testing separate indexes if the migration related to creating the new index is deprecated).