Thank you very much Andrea, Simone and Balazs. Both good information and
tips. I did not want to give to much details to start. But to answer your
questions:

1. Yes I suspected because of the nature of the GetCapabilities that mosaics
are the only way to go. 
2. Mosaics also make sense since 90% of the data is orthoimagery, 5% DEM and
about 5% a mix of vector and other formats (there are some "themes" that can
break it into different groups, but it is meant to be all the latest imagery
for whatever location is available).
3. The usage pattern is probably the key (see below). While there are a lot
of files, we expect very low server load. A few users per day who want a
specific set 5 to 10 images from a server.

The hesitation in mosaics is two-fold. One was that I did not see any good
automated way of creating the shapefiles for mosaics or ways to create the
stores for them. I do admit to being a geoserver noobie, but I do read the
documentation (600 pages) in detail, and what I am seeing is that we would
have to create an automated way of creating a shapefile with outlines for
each "theme" (10K or so files) and then submit this via the REST API to the
create store (would like an example).

The deeper reason for the hesitation in creating mosaics is that we are
really not in the position to apply a blanket rule for the prioritization of
overlapping images for a location. The user needs to be in control of this.
That is the "advantage" to ArcGIS geoserver. filtering is dynamic on
attribute type by the end user (cloud cover, quality, temporal age, or any
other meta data), 

One thing that we are considering (thinking out the box) is to place an
intercept proxy between geoserver and the GetMap requests. We would then
create on the fly the store and layer and redirect the request to geoserver.
This way would not prebuild the entire mosaic, just serve the items as
needed (and do garbage collection after a several thousand requests). The
trick will be creating the GetMap Requests for the clients (WorldWind,
Google Earth, etc. ) and crafting a pseudo-getCapabilities that will hide
what is going on behind the scenes. Any thoughts on this?



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