"manifest" should be named "run"

[Nick Moffitt]

    `mojo collect` applies the `collect` file to run the `collect` phase.
    `mojo deploy` applies the `deploy` file to run the `deploy` phase.
    `mojo verify` applies the `verify` file to run the `verify` phase.
    `mojo repo` applies the `repo` file to run the `repo` phase.
...
    `mojo run` applies the `manifest` file to run the `manifest`.

I think that "run" is a great name for this, and we all talk about "mojo runs" as things we envision in a sort of fakey CI spacetime. We inspect their jenkins output dumps and watch them as entries on the CI weather report.

To me a "manifest" is a bill of materials, listing objects contained inside a sealed vessel of some sort. What this file is doing is really writing a mojo script of sorts, and `mojo run` is the command you use. New users would find it easier to remember the connection in both directions if the manifest file were simply named `run`.

This can be brought in in a backward-compatible way: if we find a `manifest` file, we just use that, because of history. We can probably also promote *which* file gets used to a bare command-line parameter, instead of using the --manifest stuff. This feels like a more obvious CLI, to just `mojo run ./foo/bar/mything.run`.