MODE-2341 Fixed the reindexing behavior

This PR contains 2 fixes:
* the `RepositoryQueryManager` should not be marked as initialized until all components (including connectors) have finished initializing
* the `LocalIndexProvider` should always scan whenever `createIndex` is called because that means the index definition is new for the given workspace
Is the only change to lines 179-195 indentation? If so, can it be removed from the PR? Seems unnecessary and hides what really is changing.