Sadly, when I started working on MXR, I didn't have a DVCS, so I just made live changes on landfill, lots of them. One of the changes I made was to make MXR understand #include's, e.g. nsCSSFrameConstructor.cpp. This was both recognizing that a file named nsCRT.h might not live in the same directory (and where it would live), and also recognizing that a file named nsIAtom.h might really be nsIAtom.idl. If you hover over the links from the highlighted lines in MXR, you'll see that they're correct.
The first implementation of this merely ready a list of all files in the tree (.glimpse_filenames) which glimpse had generated to enable searching (and which LXR used for find). I've been trying to optimize this for a while using various tools and caching data. But essentially it meant that if there was a missed file, the entire file index would have to be read into memory, and each included file meant a linear search of that list. There's actually a file named .glimpe_filenames_index which presumably is what I would really have liked to use, but I don't know how to use it, so instead, I've made an extra index of the files list and taught MXR to use it (thankfully the code was fairly modular so I was able to drop it into a single function and everything else just worked).
Anyway, for a long time people had asked me to commit my changes to LXR back into cvs.mozilla.org, but I wasn't willing to do so until I had fixed the performance regression of my initial #include feature. This April, Benjamin landed mxr into Hg for the first time in order to enable Mozilla IT to deploy it in parallel to LXR. In July, Reed decommissioned LXR. At the end of July, while at the Summit, I started doing real optimization work using The New York Times Perl Profiler. Finally today I added what amounts to 25 lines in the source viewer and another 10 or so lines to the code which generates the index (this part of the indexing process is much faster than the step that builds the primary search index), and pages should now load nearly as fast as from LXR.