Add large ply file to be tested and minor improvement to mesh-ply.
Merge branch 'master' of https://github.com/sirikata/sirikata
Default color for ply-models is now white. Also binary ply files removed.
Add minor improvement to PlyModelSystem to display large random ply files.
Add daemon and pid-file options.

Add daemon option for requesting that the process fork, detach from
the parent and stdin/out/err, and run in the background. Add a
pid-file option to request that it write it's pid. Collect these steps
and setting the log file output into a single method,
DaemonizeAndSetOutputs and call it in all binaries before our first
output, ReportVersion.
Fix reverted externals/prox.
Larger ply files with randomly distributed coordinates show up correctly with the mesh-ply plugin.
Merge branch 'master' of https://github.com/sirikata/sirikata
Mesh-ply plugin now enables display of multiple textures and colors in certain files.
Multiple textures and colors show up with Mesh-ply plugin.
Add option to log everything to a file instead of just SILOGs.

Add an option, enabled by default, to log everything (stdout, stderr,
and SILOGs) to the log file instead of just SILOGs. It's enabled by
default since enough various things (e.g. output from scripts,
asserts, etc.) go to stdout that they need to go into log files.
Clarify a few log messages.
Merge remote branch 'origin/master' into manual-query

Conflicts:
	externals/prox
Merge branch 'master' of https://github.com/sirikata/sirikata
Fix PlyLoaderTest and add minor changes to PlyModelSystem.
Don't re-post prox updates.

We handle both ProximityResults and ProximityUpdates, but were going
through the wrong call when handling each ProximityUpdate in a
ProximityResults.
Fix thread safety when adding/removing replicas to LocationService.

In LibproxManualProximity results from other servers need to do two
things: add/remove replicas from the main LocationService and notify
the replicated trees/query handlers of the changes. These need to
happen in different threads. The LocationService operations must be in
the main strand and the replicated tree operations need to be in the
prox strand. This fixes these updates so they pass through both
strands doing the relevant work in each. Fixes a crash that was
popping up randomly under sufficient load.
Add ManualReplicatedRequestManager to track update requests that fail to apply.

Requests to update a cut may fail if the server is still waiting for
another server to return results (e.g. an OH says to refine a
replicated tree to server A, but server A is still waiting on it's
refinement command to server B to complete). To handle this, make the
server save any failed requests with a timeout and try to reapply them
when an update is received that provides new children for that node.
Work around unreliable server-server messages.

There's only one location where server-to-server messages can be
unreliable, right after they're received and pushed into a shared
queue to cross threads. Unfortunately a number of server components
really rely on message reliability and ordering. While a real
reliability layer would be preferable, handle this for now by
whitelisting everything but ODP messages to be foreced into the
queue. As long as we trust server components to behave nicely then
this should be fine for now.
Make SST's Connection::closeConnections thread safe.

Add locking to Connection::closeConnections so it's thread safe. It is
no longer only being called during the final destruction of SST data,
so it wasn't safe to assume only one thread was running code
anymore. Locking needs to be handled carefully since the mutex being
used isn't recursive. To handle this properly we remove each
connection from the set while locked, save the shared_ptr, then only
reset it after releasing the lock. Fixes #514.