pkg/climain is the flag-parsing logic for supporting Miller's command-line interface. When you type something like mlr --icsv --ojson put '$sum = $a + $b' then filter '$sum > 1000' myfile.csv, it's the CLI parser which makes it possible for Miller to construct a CSV record-reader, a transformer chain of put then filter, and a JSON record-writer.
pkg/cli contains datatypes for the CLI-parser, which was split out to avoid a Go package-import cycle.
I don't use the Go flag package. The flag package is quite fine; Miller's command-line processing is multi-purpose between serving CLI needs per se as well as for manpage/docfile generation, and I found it simplest to roll my own command-line handling here. More importantly, some Miller verbs such as sort take flags more than once -- mlr sort -f field1 -n field2 -f field3 -- which is not supported by the flag package.
Package climain contains high-level logic for parsing the main Miller
command line. Package cli contains the flags table and most handlers;
package cli is also invoked by verbs to parse their own flags.