Switch <base/cmd> to use <base/json> rather than <starsha/note> for args file parsing

This removes the only non-starsha user of \<starsha/note>.

All args files inside the codebase at present are updated in this commit.
Past experience with the exception flag have it throwing a lot of odd / hard to read exceptions. Our exceptions are a lot easier to interpret (They all end up as user facing error messages).