fix 'meteor rebuild x y z'

We weren't refreshing the package cache so it didn't rebuild
it. Simplify by getting rid of redundant code.
quiet non-errors in --from-checkout
self-test: better path to executable
Finish removing include from files.cp_r
$TREE_HASH_DEBUG
builder.copyDirectory: copy symlinks as symlink

otherwise our new change to have tool/node_modules be a symlink breaks
add XXX comment about serviceconnection timeout