chore: clean up Project.toml files

[mancellin]

I tried to clean up the dependencies in the TOML files with the following objectives:

• the main Project.toml is the bare minimum that user installing the library should have to use it. It does not come with a Manifest.toml file, since the user will use it in the environment they want.
• the test/Project.toml lists the supplementary dependencies needed to run the tests.
• the paper/Project.toml lists the supplementary dependencies to run the test cases of the paper directory. It comes with a Manifest.toml listing the exact versions of the libraries used to get these results. (I only checked a few of the scripts from this directory, feel free to update it if necessary.)