The built-in package manager has the Project.toml and Manifest.toml integrated in the notebook.jl file. If the packages are already installed, Pluto does not re-install them, analogue to activating a Project.toml file (what is actually done under the hood).
To use an external Project.toml file see here: https://github.com/fonsp/Pluto.jl/wiki/🎁-Package-management#pattern-the-shared-environment
Combining both approaches is not possible because it would be ambiguous.
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