diff --git a/main.go b/main.go
index d8b8aee9..373dd9d4 100644
--- a/main.go
+++ b/main.go
@@ -22,6 +22,7 @@ import (
 	"codemap/internal/buildinfo"
 	"codemap/internal/projectpath"
 	"codemap/limits"
+	codemapmcp "codemap/mcp"
 	"codemap/render"
 	"codemap/scanner"
 	"codemap/watch"
@@ -80,6 +81,14 @@ func main() {
 		return
 	}
 
+	if len(os.Args) >= 2 && os.Args[1] == "status" {
+		if err := runStatusSubcommand(); err != nil {
+			fmt.Fprintf(os.Stderr, "Error: %v\n", err)
+			os.Exit(1)
+		}
+		return
+	}
+
 	// Handle "watch" subcommand before flag parsing
 	if len(os.Args) >= 2 && os.Args[1] == "watch" {
 		subCmd := "status"
@@ -267,6 +276,8 @@ func main() {
 	watchMode := flag.Bool("watch", false, "Live file watcher daemon (experimental)")
 	stdinMode := flag.Bool("stdin", false, "Read file manifest from stdin (use with --deps)")
 	importersMode := flag.String("importers", "", "Check file impact: who imports it, is it a hub?")
+	hubsMode := flag.Bool("hubs", false, "List hub files (3+ importers)")
+	fileMode := flag.String("file", "", "Show imports, importers, and hub status for one file")
 	topologyMode := flag.Bool("topology", false, "Show project/module dependency topology")
 	moduleMode := flag.String("module", "", "Show context for one exact module ID or unique name")
 	moduleFileMode := flag.String("module-file", "", "Show context for the module owning a repository-relative file")
@@ -275,6 +286,9 @@ func main() {
 	flag.BoolVar(helpMode, "h", false, "Show help (shorthand)")
 	// Short flag aliases
 	flag.IntVar(depthLimit, "d", 0, "Limit tree depth (shorthand)")
+	flag.Usage = func() {
+		fmt.Fprintln(flag.CommandLine.Output(), "Run 'codemap --help' for usage.")
+	}
 	flag.Parse()
 	refExplicit := false
 	flag.Visit(func(f *flag.Flag) {
@@ -305,6 +319,8 @@ func main() {
 		fmt.Println("  --exclude <patterns> Exclude paths matching patterns (e.g., '.xcassets,Fonts')")
 		fmt.Println("  --stdin             Read JSON file manifest from stdin (use with --deps)")
 		fmt.Println("  --importers <file>  Check file impact (who imports it, hub status)")
+		fmt.Println("  --hubs              List hub files (3+ importers)")
+		fmt.Println("  --file <file>       Imports, importers, and hub status for one file")
 		fmt.Println("  --json              Output machine-readable JSON")
 		fmt.Println("  --debug             Show scanner and path diagnostics")
 		fmt.Println("  --watch             Run the live file watcher daemon")
@@ -367,6 +383,7 @@ func main() {
 		fmt.Println("  codemap context                 # Print machine-readable project context JSON")
 		fmt.Println("  codemap serve                   # Serve project intelligence over HTTP")
 		fmt.Println("  codemap version                 # Show build version")
+		fmt.Println("  codemap status                  # Version, project root, config, watch daemon")
 		fmt.Println()
 		fmt.Println("Recommended onboarding:")
 		fmt.Println("  codemap setup                   # Configure project and agent hooks")
@@ -374,12 +391,16 @@ func main() {
 		os.Exit(0)
 	}
 
-	root, importer, err := resolveImportersInvocation(flag.Arg(0), *importersMode, projectRootExplicit)
+	fileTarget := importersMode
+	if *fileTarget == "" {
+		fileTarget = fileMode
+	}
+	root, importer, err := resolveImportersInvocation(flag.Arg(0), *fileTarget, projectRootExplicit)
 	if err != nil {
 		fmt.Fprintf(os.Stderr, "Error: %v\n", err)
 		os.Exit(2)
 	}
-	*importersMode = importer
+	*fileTarget = importer
 	if root == "" {
 		root = "."
 	}
@@ -482,6 +503,18 @@ func main() {
 		runImportersMode(absRoot, *importersMode, *jsonMode, filters)
 		return
 	}
+	if *hubsMode || *fileMode != "" {
+		text, err := codemapmcp.HubsText(context.Background(), absRoot, filters)
+		if *fileMode != "" {
+			text, err = codemapmcp.FileContextText(context.Background(), absRoot, *fileMode, filters)
+		}
+		if err != nil {
+			fmt.Fprintf(os.Stderr, "Error building file graph: %v\n", err)
+			os.Exit(1)
+		}
+		fmt.Print(text)
+		return
+	}
 
 	if *moduleMode != "" && *moduleFileMode != "" {
 		fmt.Fprintln(os.Stderr, "Error: specify either --module or --module-file, not both")
@@ -646,6 +679,17 @@ func applyGlobalRootOptions(args []string) ([]string, bool, error) {
 }
 
 func resolveImportersInvocation(root, importer string, projectRootExplicit bool) (string, string, error) {
+	// A relative file names a path from the working directory, so from a
+	// subdirectory the project is still the enclosing repository.
+	if root == "" && !projectRootExplicit && importer != "" && !filepath.IsAbs(importer) {
+		if abs, err := filepath.Abs(importer); err == nil {
+			if _, err := os.Stat(abs); err == nil {
+				if inferredRoot, file, err := resolveImportersInvocation("", abs, false); err == nil {
+					return inferredRoot, file, nil
+				}
+			}
+		}
+	}
 	if root != "" || projectRootExplicit || importer == "" || !filepath.IsAbs(importer) {
 		// Canonicalize the importer so the relative path matches the
 		// canonicalized project root (e.g. macOS /tmp -> /private/tmp).
@@ -867,6 +911,31 @@ func buildImportersReport(root, file string, filters scanner.Filters) (scanner.I
 	return buildImportersReportFromGraph(root, file, fg)
 }
 
+// runStatusSubcommand is the CLI side of the MCP status tool.
+func runStatusSubcommand() error {
+	cwd, err := os.Getwd()
+	if err != nil {
+		return err
+	}
+	root, found, err := cmd.ResolveNearestGitRoot(cwd)
+	if err != nil {
+		return err
+	}
+	fmt.Printf("codemap %s\n", buildinfo.Current())
+	if !found {
+		fmt.Printf("Project root: %s (no enclosing repository)\n", cwd)
+		return nil
+	}
+	fmt.Printf("Project root: %s\n", root)
+	configPath := config.ConfigPath(root)
+	if _, err := os.Stat(configPath); err == nil {
+		fmt.Printf("Config: %s\n", configPath)
+	} else {
+		fmt.Println("Config: none (run 'codemap config init')")
+	}
+	return runWatchSubcommand("status", root)
+}
+
 func runImportersMode(root, file string, jsonMode bool, filters scanner.Filters) {
 	report, err := buildImportersReport(root, file, filters)
 	if err != nil {
diff --git a/main_cli_rough_edges_test.go b/main_cli_rough_edges_test.go
new file mode 100644
index 00000000..254cf66f
--- /dev/null
+++ b/main_cli_rough_edges_test.go
@@ -0,0 +1,111 @@
+package main
+
+import (
+	"bytes"
+	"context"
+	"os/exec"
+	"path/filepath"
+	"strings"
+	"testing"
+
+	"codemap/topology"
+)
+
+// #289: the CLI routes that the MCP server already had, and the rough edges
+// hit when running every command.
+
+func runCodemapIn(t *testing.T, dir string, args ...string) (string, string, error) {
+	t.Helper()
+	command := exec.Command(codemapTestBinaryPath, args...)
+	command.Dir = dir
+	var stdout, stderr bytes.Buffer
+	command.Stdout = &stdout
+	command.Stderr = &stderr
+	err := command.Run()
+	return stdout.String(), stderr.String(), err
+}
+
+func TestImportersFromSubdirectoryUsesEnclosingRepository(t *testing.T) {
+	repo := makeMainGitRepo(t, "main")
+	stdout, stderr, err := runCodemapIn(t, filepath.Join(repo, "pkg"), "--importers", "types/types.go")
+	if err != nil {
+		t.Fatalf("--importers from a subdirectory failed: %v\n%s", err, stderr)
+	}
+	if !strings.Contains(stdout, "pkg/types/types.go") || !strings.Contains(stdout, "HUB FILE") {
+		t.Fatalf("importers must resolve against the repository root:\n%s", stdout)
+	}
+}
+
+func TestMissingFlagValuePointsAtHelpInsteadOfDumpingUsage(t *testing.T) {
+	_, stderr, err := runCodemapWithInput("", "--importers")
+	if err == nil {
+		t.Fatal("expected a usage error")
+	}
+	if !strings.Contains(stderr, "Run 'codemap --help'") || strings.Contains(stderr, "-animate") {
+		t.Fatalf("flag error must be one hint, not the full flag dump:\n%s", stderr)
+	}
+}
+
+func TestHubsAndFileFlagsMatchMCPOutput(t *testing.T) {
+	repo := makeMainGitRepo(t, "main")
+	hubs, stderr, err := runCodemapIn(t, repo, "--hubs")
+	if err != nil {
+		t.Fatalf("--hubs failed: %v\n%s", err, stderr)
+	}
+	if !strings.Contains(hubs, "=== Hub Files (1 total) ===") || !strings.Contains(hubs, "pkg/types/types.go (4 importers)") {
+		t.Fatalf("--hubs output:\n%s", hubs)
+	}
+	file, stderr, err := runCodemapIn(t, repo, "--file", "pkg/types/types.go")
+	if err != nil {
+		t.Fatalf("--file failed: %v\n%s", err, stderr)
+	}
+	if !strings.Contains(file, "=== File Context: pkg/types/types.go ===") || !strings.Contains(file, "IMPORTED BY (4 files)") {
+		t.Fatalf("--file output:\n%s", file)
+	}
+}
+
+func TestHubsHonoursExcludeFlag(t *testing.T) {
+	repo := makeMainGitRepo(t, "main")
+	hubs, stderr, err := runCodemapIn(t, repo, "--hubs", "--exclude", "a,b")
+	if err != nil {
+		t.Fatalf("--hubs --exclude failed: %v\n%s", err, stderr)
+	}
+	if !strings.Contains(hubs, "No hub files found") {
+		t.Fatalf("--exclude must drop importers below the hub threshold:\n%s", hubs)
+	}
+}
+
+func TestStatusSubcommand(t *testing.T) {
+	repo := makeMainGitRepo(t, "main")
+	stdout, stderr, err := runCodemapIn(t, repo, "status")
+	if err != nil {
+		t.Fatalf("status failed: %v\n%s", err, stderr)
+	}
+	for _, want := range []string{"codemap ", "Project root: ", "Config: ", "Watch daemon "} {
+		if !strings.Contains(stdout, want) {
+			t.Fatalf("status output missing %q:\n%s", want, stdout)
+		}
+	}
+	help, _, _ := runCodemapWithInput("", "--help")
+	for _, want := range []string{"--hubs", "--file <file>", "codemap status"} {
+		if !strings.Contains(help, want) {
+			t.Fatalf("--help does not mention %q", want)
+		}
+	}
+}
+
+func TestTopologyWithNoModulesPointsAtDeps(t *testing.T) {
+	original := buildTopologyGraphOnly
+	buildTopologyGraphOnly = func(context.Context, string) (*topology.Graph, topology.CacheIdentity, error) {
+		return &topology.Graph{Coverage: topology.Coverage{Status: topology.CoverageUnavailable}}, topology.CacheIdentity{}, nil
+	}
+	t.Cleanup(func() { buildTopologyGraphOnly = original })
+
+	var out bytes.Buffer
+	if err := runTopologyMode(context.Background(), "/repo", "", "", "", false, &out); err != nil {
+		t.Fatal(err)
+	}
+	if !strings.Contains(out.String(), "Modules: 0") || !strings.Contains(out.String(), "codemap --deps") {
+		t.Fatalf("empty topology must explain itself:\n%s", out.String())
+	}
+}
diff --git a/mcp/main.go b/mcp/main.go
index 452ce56a..6f93699a 100644
--- a/mcp/main.go
+++ b/mcp/main.go
@@ -1421,17 +1421,26 @@ func handleGetHubs(ctx context.Context, req *mcp.CallToolRequest, input PathInpu
 	if invalid != nil {
 		return invalid, nil, nil
 	}
-	fg, err := scanner.BuildFileGraph(ctx, absRoot, scanner.ConfiguredFilters(absRoot))
+	text, err := HubsText(ctx, absRoot, scanner.ConfiguredFilters(absRoot))
 	if err != nil {
 		if cancelled := cancellationResult(ctx, "Hub analysis"); cancelled != nil {
 			return cancelled, nil, nil
 		}
 		return errorResult("Failed to build file graph: " + err.Error()), nil, nil
 	}
+	return textResult(text), nil, nil
+}
+
+// HubsText renders the get_hubs report; the CLI --hubs flag prints it too.
+func HubsText(ctx context.Context, absRoot string, filters scanner.Filters) (string, error) {
+	fg, err := scanner.BuildFileGraph(ctx, absRoot, filters)
+	if err != nil {
+		return "", err
+	}
 
 	hubs := fg.HubFiles()
 	if len(hubs) == 0 {
-		return textResult("No hub files found (no files with 3+ importers)." + mcpCoverageText(fg.Coverage)), nil, nil
+		return "No hub files found (no files with 3+ importers)." + mcpCoverageText(fg.Coverage), nil
 	}
 
 	// Sort by importer count
@@ -1460,7 +1469,7 @@ func handleGetHubs(ctx context.Context, req *mcp.CallToolRequest, input PathInpu
 		}
 	}
 
-	return textResult(sb.String() + mcpCoverageText(fg.Coverage)), nil, nil
+	return sb.String() + mcpCoverageText(fg.Coverage), nil
 }
 
 func handleGetFileContext(ctx context.Context, req *mcp.CallToolRequest, input ImportersInput) (*mcp.CallToolResult, any, error) {
@@ -1471,16 +1480,25 @@ func handleGetFileContext(ctx context.Context, req *mcp.CallToolRequest, input I
 	if invalid != nil {
 		return invalid, nil, nil
 	}
-	filters := scanner.ConfiguredFilters(absRoot)
-	fg, err := scanner.BuildFileGraph(ctx, absRoot, filters)
+	text, err := FileContextText(ctx, absRoot, input.File, scanner.ConfiguredFilters(absRoot))
 	if err != nil {
 		if cancelled := cancellationResult(ctx, "File context analysis"); cancelled != nil {
 			return cancelled, nil, nil
 		}
 		return errorResult("Failed to build file graph: " + err.Error()), nil, nil
 	}
+	return textResult(text), nil, nil
+}
 
-	file := normalizeImporterFile(absRoot, input.File)
+// FileContextText renders the get_file_context report; the CLI --file flag
+// prints it too.
+func FileContextText(ctx context.Context, absRoot, file string, filters scanner.Filters) (string, error) {
+	fg, err := scanner.BuildFileGraph(ctx, absRoot, filters)
+	if err != nil {
+		return "", err
+	}
+
+	file = normalizeImporterFile(absRoot, file)
 	imports := append([]string(nil), fg.Imports[file]...)
 	importers := append([]string(nil), fg.Importers[file]...)
 	isHub := fg.IsHub(file)
@@ -1498,7 +1516,7 @@ func handleGetFileContext(ctx context.Context, req *mcp.CallToolRequest, input I
 	if len(imports) == 0 && len(importers) == 0 {
 		if why, unindexed := fg.ExplainUnindexed(file, filters); unindexed {
 			sb.WriteString(notIndexedText(file, why, fg))
-			return textResult(sb.String()), nil, nil
+			return sb.String(), nil
 		}
 	}
 
@@ -1534,7 +1552,7 @@ func handleGetFileContext(ctx context.Context, req *mcp.CallToolRequest, input I
 	sb.WriteString(fmt.Sprintf("CONNECTED: %d files in dependency graph\n", len(connected)))
 	sb.WriteString(mcpCoverageText(fg.FileCoverage(file)))
 
-	return textResult(sb.String()), nil, nil
+	return sb.String(), nil
 }
 
 // handleGetWorkingSet returns the current session's working set
diff --git a/mcp/surface_hygiene_test.go b/mcp/surface_hygiene_test.go
index a49dd156..67eef082 100644
--- a/mcp/surface_hygiene_test.go
+++ b/mcp/surface_hygiene_test.go
@@ -76,8 +76,8 @@ func TestTextResultCallerClassification(t *testing.T) {
 		"handleStartWatch":      {3, 0},
 		"handleStopWatch":       {3, 0},
 		"handleGetActivity":     {2, 0},
-		"handleGetHubs":         {2, 0},
-		"handleGetFileContext":  {2, 0},
+		"handleGetHubs":         {1, 0},
+		"handleGetFileContext":  {1, 0},
 		"handleGetWorkingSet":   {2, 0},
 		"handleListSkills":      {2, 0},
 		"handleGetSkill":        {1, 0},
diff --git a/topology/format.go b/topology/format.go
index c0603379..0bb90947 100644
--- a/topology/format.go
+++ b/topology/format.go
@@ -8,10 +8,12 @@ import (
 	"strings"
 )
 
+const noModulesHint = "No modules found: topology reads multi-module manifests (Gradle, Maven, sbt, SwiftPM, Python). For a single-module project use 'codemap --deps'.\n"
+
 func FormatGraph(graph *Graph, ecosystem string) string {
 	graph = FilterGraph(graph, ecosystem)
 	if graph == nil {
-		return "PROJECT TOPOLOGY\nCoverage: unavailable\nModules: 0\n"
+		return "PROJECT TOPOLOGY\nCoverage: unavailable\nModules: 0\n" + noModulesHint
 	}
 
 	var builder strings.Builder
@@ -22,6 +24,9 @@ func FormatGraph(graph *Graph, ecosystem string) string {
 	if len(graph.Coverage.Issues) > 0 {
 		_, _ = fmt.Fprintf(&builder, "Coverage notes: %d\n", len(graph.Coverage.Issues))
 	}
+	if len(graph.Nodes) == 0 {
+		builder.WriteString(noModulesHint)
+	}
 	builder.WriteString("\n")
 
 	for _, id := range sortedNodeIDs(graph.Nodes) {