Is that needed at all? The deps aren't missing in that case, and RecomputeOutputDirty() returning true should prevent a Clean in that case anyways (?)

I thought there would be only one place that sets depfile_missing_: the block at the top of RecomputeDirty().

(Do you use IRC? Maybe this is faster to discuss over chat, #ninja-build on irc.oftc.net – but we're probably 12 timezones apart.)