Currently, indexes are built asynchronously. That is, if an index definition is added, the index is eventually built, but it's quite hard to say when it is ready for queries. This can be specially a problem right after the initial repository initialization, or after an upgrade.
In theory, system startup could be delayed until all indexes are ready (e.g. set the "reindex" flag for important indexes, and at startup, wait until the "reindex" flag is set to "false"). However, doing that would block threads that don't need an index. It would be better to only block threads that actually do run queries. That would make startup deterministic, without delaying other threads unnecessarily.
To solve the problem, we can add a property "waitForIndex" in the index definition (just Lucene indexes is fine for now, as those are the important asynchronous ones). If set, then queries that potentially use those indexes are delayed, until the indexes are ready for sure. Reindex would need to remove that property (the same as it removes e.g. refresh or sets reindex to false). For added security, queries are only blocked as long as "reindex" is also set to true (this ensures that waitForIndex is removed eventually), and waiting should time out after 2 minutes, to ensure the feature doesn't block startup forever if indexing fails for some reason.