Refactor k-mer index management with subcommands and enhanced metadata support

This commit refactors the k-mer index management tools to use a unified subcommand structure with obik, adds support for per-set metadata and ID management, enhances the k-mer set group builder to support appending to existing groups, and improves command-line option handling with a new global options registration system.

Key changes:
- Introduce obik command with subcommands (index, ls, summary, cp, mv, rm, super, lowmask)
- Add support for per-set metadata and ID management in kmer set groups
- Implement ability to append to existing kmer index groups
- Refactor option parsing to use a global options registration system
- Add new commands for listing, copying, moving, and removing sets
- Enhance low-complexity masking with new options and output formats
- Improve kmer index summary with Jaccard distance matrix support
- Remove deprecated obikindex and obisuperkmer commands
- Update build process to use the new subcommand structure

pkg/obioptions/subcommand.go

@@ -0,0 +1,43 @@
+package obioptions
+
+import (
+	"github.com/DavidGamba/go-getoptions"
+)
+
+// GenerateSubcommandParser creates an option parser that supports subcommands
+// via go-getoptions' NewCommand/SetCommandFn/Dispatch API.
+//
+// The setup function receives the root *GetOpt and should register subcommands
+// using opt.NewCommand(). Global options (--debug, --max-cpu, etc.) are
+// registered before setup is called and are inherited by all subcommands.
+//
+// Returns the root *GetOpt (needed for Dispatch) and an ArgumentParser
+// that handles parsing and post-parse processing.
+func GenerateSubcommandParser(
+	program string,
+	documentation string,
+	setup func(opt *getoptions.GetOpt),
+) (*getoptions.GetOpt, ArgumentParser) {
+
+	options := getoptions.New()
+	options.Self(program, documentation)
+	options.SetMode(getoptions.Bundling)
+	options.SetUnknownMode(getoptions.Fail)
+
+	// Register global options (inherited by all subcommands)
+	RegisterGlobalOptions(options)
+
+	// Let the caller register subcommands
+	setup(options)
+
+	// Add automatic help subcommand (must be after all commands)
+	options.HelpCommand("help", options.Description("Show help for a command"))
+
+	parser := func(args []string) (*getoptions.GetOpt, []string) {
+		remaining, err := options.Parse(args[1:])
+		ProcessParsedOptions(options, err)
+		return options, remaining
+	}
+
+	return options, parser
+}