Get run-tools-tests.sh passing.

In addition to minor "make the tests match the code" changes, there's also:

 - missing require('tar') in tarball download code
 - fix an fd leak in the bundler that was causing EMFILE on mac
 - switch run.js to listening for 'exit' to 'close' so that the end
   of stdout/err can be read
 - some concerningly necessary deletions of .build directories

Also, the version of cli-test.sh that runs against a fixed release is disabled,
since we're not building releases with the new package format for now.
Progress towards deploying apps to galaxy

Mostly changing "service" to "app"
Put ctl in meteor instead of galaxy
Factor out most of ctl into a ctl-helper package

We use ctl-helper on galaxy in the proxy control program.
Send port to proxy as Number, not string
Prevent ctl from choosing a port at random.

When deploying an app to galaxy, localPort: 0 in the deployConfig was overriding
the port assigned by satellite to the server, so the server's port was being
chosen at random, so I removed localPort from the deployConfig. (Not 100% sure
this is the right fix.)
Deploying a simple app to galaxy works now, woohoo!
Merge remote-tracking branch 'origin/linker' into server-static-resources
Allow you to directly deploy a star file
Export mongo timestamp type
Merge remote-tracking branch 'origin/linker' into server-static-resources
Specify static resources directory in server manifest

Also a few bug fixes (private/ directory was being scanned for source files,
private/ files were being included in any server target including ctl).