This answers most of your questions:
https://juliacomputing.com/blog/2018/10/16/juliapro.html
A similar thread about this issue (that also included that link):
The only question not covered there is:
Project.toml has the list of direct dependencies in the environment (those that you can load with using or import, and can also see in ]status). Installed packages also include indirect dependencies, which are listed in Manifest.toml.
All added packages and their dependencies are installed in .julia/packages, if you want to know the path to them, but you shouldn’t normally have to deal with that. You can leave the job to the Julia package manager.
More about this in the Julia manual:
https://docs.julialang.org/en/v1/manual/code-loading/