Please note, I would like to clarify a bit how this thing is being
put together.  I noticed some confusion this past week.

In the ideal world (a bit in the future) y'all as 'third party developers'
could construct your data sets as independent track hubs all in your
own domains, data storage systems, and apache servers.  Such track
hubs (shortly, with future additions to the genome browser) could then
be displayed along with the assembly hubs I have constructed and everything
together would be a single URL reference which could be in a table
of 'mouse strain data' for users to get to everything.  Everything
would be seamless, it would all appear as one set of data in the
genome browser.

We have one feature currently missing that doesn't allow this, and that
is the connection of a track hub to an existing assembly hub.  That feature
is shortly in the future.

As the current work-around, here is what I am doing.

You can still develop your data sets independently, in your own
data storage systems on the /hive/, just make sure it is known that
such data sets and areas are off limits to changes once you have them in
place.  This is the way all data for the genome browser is done,
it sits on /hive/ in a known location and doesn't change after
it is done and released.  You would be doing this even in the ideal
world where a track hub could connect to an assembly hub.

The trick now is that I symlink your data set into the constructed
assembly hub hierarchy and add an 'include' statement into the
master trackDb.txt for each assembly to include your trackDb.txt
definitions *AND HTML TRACK DESCRIPTION* files for your data sets.
With these symlinks in place and that include statement for the trackDb.txt
track definition, your data set appears in the assembly hub as part
of the assembly hub.  It isn't separate at all, it is part of
the assembly hub.  During this development phase, with the symlinks
in place you can tweak your data and your trackDb.txt definitions
and view them on hgwdev via the access portal:
  http://genome-test.soe.ucsc.edu/gbdb/hubs/mouseStrains/hgwdev.hubIndex.html

This is the special 'development' access point to make it use the
files as they exist on hgwdev. The 'public' portal access point:
  http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hubIndex.html
also known on hgwdev as:
  http://genome-test.soe.ucsc.edu/gbdb/hubs/mouseStrains/hubIndex.html
causes all references to go to the public released data which sits on
hgdownload.  The hgdownload data is a copy of the development data from
hgwdev /hive/ filesystem.  This is how a 'release' of the data is done,
it is copied from the /hive/ to hgdownload.  During our development we
can update the hgdownload data as necessary to see what it really looks
like to the public and verify all links function correctly.  As long
as all links are relative correctly, they will work on both machines.

But once we are done and the release is finished, the copy on hgdownload
becomes 'static' in the sense that we will not update it unless we really
need to make a change for some good reason.  And the development data
on hgwdev /hive/ after this release needs to be left alone as it represents
the backup second copy of the public data.

By the time we are all done with this, we will most likely have in place
that feature of allowing track hubs to connect to an assembly hub, and then
external third party developers can add their own track hubs to our existing
assembly hub.

FYI: My construction of the assembly hub is taking place on hgwdev in:
      /hive/data/genomes/asmHubs/
The development data is constructed in:
      /hive/data/genomes/asmHubs/genbank/vertebrate_mammalian/Mus*/...
which represents the hierarchy of released data files from the NCBI assembly
FTP site.  There is a set of auto scripts in the source tree that builds
all of the required assembly hub files in that development data hierarchy:
     ~/kent/src/hg/utils/automation/asmHub*
which are used in turn for each step by the master control script:
     ~/kent/src/hg/utils/automation/doAssemblyHub.pl

The final layout of the assembly hub files takes place in:
     /hive/data/genomes/asmHubs/hubLinks/
which is a set of symlinks into the development data to make only
the required files for the assembly hub to appear as one hierarchy.
This is where the symlinks to your data files would be found.

Finally, there are a few symlinks from:
    /gbdb/hubs/mouseStrains/ to /hive/data/genomes/asmHubs/hubLinks/
to make the assembly hub appear at this known URL location for
the genome-test Apache server.