Currently the fine-grained deps cache file for a module contains all the
fine-grained dependencies from the module (that is, those whose
targets are in the module). This has the advantage that producing fine-grained
dependency cache files is nicely localized (just run it on a module), but
the downside that loading the fine-grained deps cache is a global operation,
requiring every cache file to be loaded.

To improve daemon performance, we invert this, and have the deps cache file
for a module contain the fine-grained dependencies to the module. This
complicates creating the cache files: we need to explicitly sort out triggers
into the appropriate cache file.

This, then, allows us to postpone loading deps cache files until the module
is updated.

Because protocol dependencies now get sorted out into modules like everything
else, this notionally eliminates the special protocol deps cache. In practice, the
protocol deps cache has morphed in a cache for 'extra' dependencies that weren't
placed somewhere else (either because the module doesn't exist or because they
were added in an incremental run) and the meta file for it has grown additional
metadata to check consistency of the deps cache. (Because deps files are now
written after metadata, we can't store info about the in the metadata files.)