I have a large amount of code that I\'m running doxygen against. To improve performance I\'m trying to break it into modules and merge the result into one set of docs. I t
I suggest you read this topic on how I recommend to use tag files and the conditions that should apply: https://stackoverflow.com/a/8247993/784672
To answer your first question: doxygen will in general not merge the various index files together (then no performance would be gained). Although for a part you can still get external members in the index by setting ALLEXTERNALS
to YES
.
Doxygen will (auto)link symbols from other sources imported via a tag file. So in general you should divide your code into more or less self-contained modules/components/libraries, and if one such module depends on another, then import its tag file so that doxygen can link to the other documentation set. If you run doxygen twice (once for the tag file and once for the documentation) you can also resolve cyclic dependencies if you have them.
In my case I made a custom index page with links to all modules, and made a custom entry in the menu of each generated page that linked back to this index (see http://www.doxygen.nl/manual/customize.html#layout) how to add a user defined entry to the navigation menu/tree.