Codegen options should be per-proc

With multi-proc codegen (#950) the current system applies the same codegen option to each proc, but you may want each proc to have its own settings (e.g. pipeline depth set per-proc, I/O flopping, etc.).

Some options might make sense to move out of flags into source. Some options should be moved into a map that has instance-path keys and options as values.

If we want to build options programmatically, we may want an options-proto-builder to help manage the complexity.