Change a couple behaviors for optional externals

When "-o" isn't given that status of optional externals isn't reported on. I'd like to see a warning given that mentions these weren't checked out (at least for normal level of output logging).

I'd also like to see a README placed in the optional directory, that says (this directory wasn't checked out, please rerun checkout_externals at the top level with the "-o" option to make this happen if you need this directory).

I think the behavior should also be that if the directory doesn't exist it does the above creating the directory and adding a README file. But, if the directory does exist, it should ignore it (as presumably you ran checkout_externals with a "-o" option previously. But, it should normally print a warning if this is happening (for example "leaving the existing optional external directory tools/PTCLM since it already exists and you didn't specify the "-o" option).

Start by locating the checkout_externals handling for the "-o" option and optional directories. Confirm how missing and existing optional directories are processed, then implement the requested warnings and README behavior. Done means normal output reports skipped externals and missing directories receive the specified README without overwriting existing directories.

Written by the indexing model from the issue text.