cli: Add ability to side-load stones while vessel is running

[ermo]

Sometimes, it is necessary to side-load .stones in one go due to wanting to have an atomic index update.

This ticket is about having the option of:

1. Side-loading stones (which should only happen if summit has stopped pushing builds AND summit no longer fires the "refresh the git repo" event timer.
2. Choosing whether the index should be updated after each .stone XOR only after all stones have been side-loaded

This is a primitive that can later be used as the basis for the idea of "build sets", which are a group of recipes that need to be built against the same upstream git ref and must not be included in each other's dep graph (so no index updates after each has been built).

Depends on #75 and #76