Subsets of dependencies with packrat

We should consider whether it would be fruitful to allow packrat to manage only a subset of dependencies. Instead of inferring the set of dependencies from the project context, we might allow the user to specify which packages should be managed by packrat.

Alternatively, we can specify a set of packages which we are comfortable loading from the user library, and can exclude from packrat.

This is less useful from the 'reproducibility' perspective, but makes sense for e.g. package development where you might want to develop / test against the development version of certain packages, but still feel comfortable using other 'release' version of packages in the user library.

Similarly, we might want to avoid having copies of very large packages (e.g. BioConductor annotation packages) in each project, if there are multiple projects using the same data.

No files, tests, or entry points are named. Start by reviewing how packrat currently infers project dependencies and selects packages for management, then compare the proposed subset and user-library exclusion approaches. Done would require an agreed design, implemented behavior, and tests covering the chosen dependency-selection rules.