stage2: CacheMode.whole fixes

 * Logic to check whether a bin file is not emitted is more complicated
   in between `Compilation.create` and `Compilation.update`. Fixed the
   logic that decides whether to build compiler-rt and other support
   artifacts.
 * Basically, one cannot inspect the value of `comp.bin_file.emit` until
   after update() is called - fixed another instance of this happening
   in the CLI.
 * In the CLI, `runOrTest` is updated to properly use the result value
   of `comp.bin_file.options.emit` rather than guessing whether the
   output binary is.
 * Don't assume that the emit output has no directory components in
   sub_path. In other words, don't assume that the emit directory is the
   final directory; there may be sub-directories.

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