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.