Update Makefile to handle the import in `plaintext.proto`.
Import path is modified to be relative to the project root.
And we run `protoc` from where `Makefile` locates, i.e. the project
root.
Reference:
- plaintext.proto: 62b2c6c482/sec/insecure/pb/plaintext.proto
In isort, black, and flake8, respectively.
Add `format` in Makefile
Run top level packages only
With `setup.py`, to avoid running other unrelated directories.
Refactor
