After half of year of experience with clang based indexer (thing that makes navigator and usage possible by scanning all source files) I have decided to introduce new default "relaxed" mode. In this mode, header based dependecies are ignored - means if you change a header, indexer will reindex just that single header and not every file that depends on that header.
The rational is that when working on some deep interface and changing header and associated files, changing header chokes the whole system by reindexing too many files, many of them in no need of reindexing (usually the change of header affects just implementation file at max). So we are trading here something like 0.1% of inaccuracy for 1000% increase in throughput..
Trying that for more than month, I think this new mode is superior and it is now default. You still have the option to reindex all files (in Assist menu) in cases it misbehaves (did not happen yet though).