Improve file enumeration in generate subcommand

[mattt]

This PR makes a few small changes to improve the ergonomics and performance of the generate subcommand:

First, we pass .isDirectoryKey into the includingPropertiesForKeys argument when constructing a file enumerator. I haven't profiled this, but it should be faster for the file manager to pick this up during enumeration rather than fetching it in the loop on-demand.

Second, we pass .skipsHiddenFiles and .skipsPackageDescendants as enumeration options. Among other things, this prevents cloned dependencies in .swiftpm from being pulled in when passing the current directory (.) as an input argument.

Third, we tell the file enumerator to skip the top-level Tests/ directory. In the future, we may replace this with code that parses the Package.swift manifest file and identifies the source files directly.