Refactor file structure of PROBE source

[charmoniumQ]

I took the opportunity after a somewhat stressful US-RSE and prelim exam mitigate technical debt in PROBE. One source of such debt is that I kept throwing source code in the repository. It used be called "Rust Prov-Tracer", and some of the directories that made sense then obviously don't any more. probe_src doesn't make as much sense as I thought. Hopefully the refactor fixes this issues and makes the repository easier to understand.

Since this PR touches a lot of files, it will create a lot of merge conflicts. I want to put that burden of resolving those on myself rather than on you, because I probably have more time to deal with that. We will try to merge all of the currently alive PRs before this one. Please let me know if you have any un-pushed PRs.

[charmoniumQ]

Q: How to review this massive PR that touches almost every file?

A: Skip the file moves and deletions at first. Look only at the changes. Those are relatively minimal.

Then, look at the final directory structure; don't look at each individual move. Also see the new README.md's explanation of the directory structure.