CLI cleanup: production-ready file-mode workflow

Production-readiness cleanup for the local file-mode CLI workflow. Removes legacy --three-file support, fixes daemon Ctrl-C cleanup, hardens shard cache correctness, fixes restore --local counting/exclusions, and verifies update/setup/file-mode command surface.

Author: jonathanpopham

README.md

@@ -110,31 +110,15 @@ Manages `.graph.*` shards written next to each source file. Agents read these wi
 
 | Command | Description |
 |---|---|
-| `analyze [path]` | Upload repo, run full analysis, write graph files (use `--three-file` for best results, `--no-shards` to skip) |
+| `analyze [path]` | Upload repo, run full analysis, write `.graph.*` files (`--no-shards` skips file writing) |
 | `skill` | Print agent awareness prompt — pipe to `CLAUDE.md` or `AGENTS.md` |
-| `watch [path]` | Generate graph files on startup, then keep them updated incrementally |
+| `supermodel` | Generate graph files on startup, then keep them updated incrementally |
 | `clean [path]` | Remove all `.graph.*` files from the repository |
-| `hook` | Claude Code `PostToolUse` hook — forward file-change events to the `watch` daemon |
+| `hook` | Claude Code `PostToolUse` hook — forward file-change events to the `supermodel` daemon |
 
-### Three-file shard format (recommended)
+### Tell your agent about graph files
 
-For best results, use the `--three-file` flag to generate separate `.calls`, `.deps`, and `.impact` files instead of a single `.graph` file:
-
-```bash
-supermodel analyze --three-file
-```
-
-This produces three files per source file:
-
-```
-src/cache.go          → src/cache.calls.go    # who calls what, with file:line
-                      → src/cache.deps.go     # imports and imported-by
-                      → src/cache.impact.go   # risk level, domains, blast radius
-```
-
-The three-file format is **68% faster** in benchmarks because grep hits are more targeted — searching for a function name hits only the `.calls` file with caller/callee data, not a combined blob.
-
-**Tell your agent about the files** by adding this to `CLAUDE.md` or `AGENTS.md`:
+Add the Supermodel graph-file prompt to `CLAUDE.md`, `AGENTS.md`, or your agent's instruction file:
 
 ```bash
 supermodel skill >> CLAUDE.md

cmd/analyze.go

@@ -1,8 +1,6 @@
 package cmd
 
 import (
-	"fmt"
-
 	"github.com/spf13/cobra"
 
 	"github.com/supermodeltools/cli/internal/analyze"
@@ -13,7 +11,6 @@ import (
 func init() {
 	var opts analyze.Options
 	var noShards bool
-	var threeFile bool
 
 	c := &cobra.Command{
 		Use:   "analyze [path]",
@@ -35,9 +32,6 @@ Use --no-shards to skip writing graph files.`,
 			if err := cfg.RequireAPIKey(); err != nil {
 				return err
 			}
-			if noShards && threeFile {
-				return fmt.Errorf("--three-file cannot be used with --no-shards")
-			}
 			dir := "."
 			if len(args) > 0 {
 				dir = args[0]
@@ -46,7 +40,7 @@ Use --no-shards to skip writing graph files.`,
 				// Shard mode: Generate handles the full pipeline (API call +
 				// cache + shards) in a single upload. Running analyze.Run
 				// first would duplicate the API call.
-				return shards.Generate(cmd.Context(), cfg, dir, shards.GenerateOptions{Force: opts.Force, ThreeFile: threeFile})
+				return shards.Generate(cmd.Context(), cfg, dir, shards.GenerateOptions{Force: opts.Force})
 			}
 			return analyze.Run(cmd.Context(), cfg, dir, opts)
 		},
@@ -55,7 +49,6 @@ Use --no-shards to skip writing graph files.`,
 	c.Flags().BoolVar(&opts.Force, "force", false, "re-analyze even if a cached result exists")
 	c.Flags().StringVarP(&opts.Output, "output", "o", "", "output format: human|json")
 	c.Flags().BoolVar(&noShards, "no-shards", false, "skip writing .graph.* shard files")
-	c.Flags().BoolVar(&threeFile, "three-file", false, "generate .calls/.deps/.impact files instead of single .graph")
 
 	rootCmd.AddCommand(c)
 }

cmd/hook.go

@@ -11,14 +11,14 @@ func init() {
 
 	c := &cobra.Command{
 		Use:   "hook",
-		Short: "Forward Claude Code file-change events to the watch daemon",
-		Long:  `Reads a Claude Code PostToolUse JSON payload from stdin and forwards the file path to the running watch daemon via UDP. Install as a PostToolUse hook in .claude/settings.json.`,
+		Short: "Forward Claude Code file-change events to the Supermodel daemon",
+		Long:  `Reads a Claude Code PostToolUse JSON payload from stdin and forwards the file path to the running Supermodel daemon via UDP. Install as a PostToolUse hook in .claude/settings.json.`,
 		Args:  cobra.NoArgs,
 		RunE: func(cmd *cobra.Command, args []string) error {
 			return shards.Hook(port)
 		},
 	}
 
-	c.Flags().IntVar(&port, "port", 7734, "UDP port of the watch daemon")
+	c.Flags().IntVar(&port, "port", 7734, "UDP port of the Supermodel daemon")
 	rootCmd.AddCommand(c)
 }

cmd/login.go

@@ -17,7 +17,7 @@ func init() {
 For CI or headless environments, pass the key directly:
   supermodel login --token smsk_live_...`,
 		RunE: func(cmd *cobra.Command, _ []string) error {
-			if token != "" {
+			if cmd.Flags().Changed("token") {
 				return auth.LoginWithToken(token)
 			}
 			return auth.Login(cmd.Context())

cmd/root.go

@@ -1,8 +1,10 @@
 package cmd
 
 import (
+	"context"
 	"fmt"
 	"os"
+	"os/signal"
 	"syscall"
 	"time"
 
@@ -176,8 +178,22 @@ func init() {
 
 // Execute is the entry point called by main.
 func Execute() {
+	ctx, stop := signal.NotifyContext(context.Background(), os.Interrupt, syscall.SIGTERM)
+	done := make(chan struct{})
+	go func() {
+		select {
+		case <-ctx.Done():
+			stop()
+		case <-done:
+		}
+	}()
+	rootCmd.SetContext(ctx)
 	if err := rootCmd.Execute(); err != nil {
 		fmt.Fprintln(os.Stderr, err)
+		close(done)
+		stop()
 		os.Exit(1)
 	}
+	close(done)
+	stop()
 }