Optional dependencies

Some app dependencies are truly optional in the sense that the feature may not be used by all and might be better as an opt in, e.g., shake-n-break structure edits, UPF-tools for UPF inspection on pseudo uploads, etc. Perhaps best to make these officially optional (see #1512 for an example implementation, which we could extend to be more user friendly via helpful messages when a package is missing). At least in the case of shake-n-break, the package pulls in many dependencies!