cmd

var RootCmd = &cobra.Command{
	Use:   "iccheck",
	Short: "Finds inconsistent changes in your git changes",
	Long: fmt.Sprintf(`ICCheck %v
Finds inconsistent changes in your git changes.`, cli.GetFormattedVersion()),
	Version:      cli.GetFormattedVersion(),
	SilenceUsage: true,
	RunE: func(cmd *cobra.Command, args []string) error {
		ctx, cancel := context.WithTimeout(context.Background(), time.Second*time.Duration(timeoutSeconds))
		defer cancel()

		if err := setLogLevel(); err != nil {
			return err
		}
		repoDir, err := getRepoDir()
		if err != nil {
			return err
		}
		repo, err := git.PlainOpen(repoDir)
		if err != nil {
			return errors.Wrapf(err, "opening repository at %v", repoDir)
		}
		searchConf, err := searchConfig(repoDir)
		if err != nil {
			return err
		}

		if fromRef == "" && toRef != "" {

			fromRef = toRef + "^"
		} else if fromRef != "" && toRef == "" {
			return errors.New("only one of --from was set, this is invalid - do not set for automatic discovery or set both")
		} else if fromRef == "" && toRef == "" {
			fromRef, toRef, err = autoDetermineRefs(repo)
			if err != nil {
				return errors.Wrapf(err, "determining refs")
			}
		}

		fromTree, err := resolveTree(repo, fromRef)
		if err != nil {
			return errors.Wrap(err, "resolving base tree")
		}
		toTree, err := resolveTree(repo, toRef)
		if err != nil {
			return errors.Wrap(err, "resolving target tree")
		}

		queries, changedFiles, err := search.DiffTrees(ctx, fromTree, toTree)
		if err != nil {
			return err
		}
		slog.Info(fmt.Sprintf("%d changed text chunk(s) were found within %d changed file(s).", len(queries), changedFiles), "from", fromTree, "to", toTree)
		for i, q := range queries {
			slog.Debug(fmt.Sprintf("Query#%d", i), "query", q)
		}
		cloneSets, err := search.Search(ctx, algorithm, queries, toTree, searchConf)
		if err != nil {
			return err
		}
		reportClones(cloneSets)
		return nil
	},
}