diff --git a/internal/canonical/secrets.go b/internal/canonical/secrets.go
new file mode 100644
index 0000000..84441c1
--- /dev/null
+++ b/internal/canonical/secrets.go
@@ -0,0 +1,74 @@
+package canonical
+
+import (
+	"fmt"
+
+	"github.com/lukaszraczylo/harness-sync/internal/secrets"
+)
+
+// SubstituteSecrets walks the bundle and replaces ${VAR} placeholders in all
+// config fields using lookup. Skill/agent/instruction bodies are intentionally
+// NOT substituted — they are content, not config.
+//
+// Returns an error (wrapping the offending field path) if any referenced
+// variable is missing from lookup.
+func SubstituteSecrets(b *Bundle, lookup secrets.Lookup) error {
+	var err error
+
+	// Gateway
+	if b.Profile.Gateway.Token, err = sub(lookup, "profile.gateway.token", b.Profile.Gateway.Token); err != nil {
+		return err
+	}
+	if b.Profile.Gateway.URL, err = sub(lookup, "profile.gateway.url", b.Profile.Gateway.URL); err != nil {
+		return err
+	}
+	if b.Profile.Gateway.DefaultModel, err = sub(lookup, "profile.gateway.default_model", b.Profile.Gateway.DefaultModel); err != nil {
+		return err
+	}
+
+	// Upstreams
+	for i := range b.Profile.Upstreams {
+		u := &b.Profile.Upstreams[i]
+		field := fmt.Sprintf("profile.upstreams[%d](%s)", i, u.Name)
+		if u.APIKey, err = sub(lookup, field+".api_key", u.APIKey); err != nil {
+			return err
+		}
+		if u.BaseURL, err = sub(lookup, field+".base_url", u.BaseURL); err != nil {
+			return err
+		}
+	}
+
+	// MCP servers
+	for i := range b.MCP.Servers {
+		sv := &b.MCP.Servers[i]
+		field := fmt.Sprintf("mcp.servers[%d](%s)", i, sv.Name)
+
+		if sv.Command, err = sub(lookup, field+".command", sv.Command); err != nil {
+			return err
+		}
+		if sv.URL, err = sub(lookup, field+".url", sv.URL); err != nil {
+			return err
+		}
+		for j, arg := range sv.Args {
+			if sv.Args[j], err = sub(lookup, fmt.Sprintf("%s.args[%d]", field, j), arg); err != nil {
+				return err
+			}
+		}
+		for k, v := range sv.Env {
+			if sv.Env[k], err = sub(lookup, fmt.Sprintf("%s.env[%s]", field, k), v); err != nil {
+				return err
+			}
+		}
+	}
+
+	return nil
+}
+
+// sub applies secrets.Substitute and wraps errors with field context.
+func sub(lookup secrets.Lookup, field, value string) (string, error) {
+	result, err := secrets.Substitute(value, lookup)
+	if err != nil {
+		return "", fmt.Errorf("%s: %w", field, err)
+	}
+	return result, nil
+}
diff --git a/internal/canonical/secrets_test.go b/internal/canonical/secrets_test.go
new file mode 100644
index 0000000..54f4ab9
--- /dev/null
+++ b/internal/canonical/secrets_test.go
@@ -0,0 +1,101 @@
+package canonical
+
+import (
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+)
+
+// lookup returns env values from the provided map; missing keys return false.
+func mapLookup(m map[string]string) func(string) (string, bool) {
+	return func(name string) (string, bool) {
+		v, ok := m[name]
+		return v, ok
+	}
+}
+
+func TestSubstituteSecretsGatewayToken(t *testing.T) {
+	b := &Bundle{
+		Profile: Profile{
+			Name: "test",
+			Gateway: Gateway{
+				Token: "${MY_TOKEN}",
+				URL:   "https://gw.lan",
+			},
+		},
+	}
+	err := SubstituteSecrets(b, mapLookup(map[string]string{"MY_TOKEN": "secret123"}))
+	require.NoError(t, err)
+	assert.Equal(t, "secret123", b.Profile.Gateway.Token)
+	assert.Equal(t, "https://gw.lan", b.Profile.Gateway.URL)
+}
+
+func TestSubstituteSecretsUpstreamAPIKey(t *testing.T) {
+	b := &Bundle{
+		Profile: Profile{
+			Name: "test",
+			Upstreams: []Upstream{
+				{Name: "openai", APIKey: "${OPENAI_KEY}", BaseURL: "https://api.openai.com"},
+			},
+		},
+	}
+	err := SubstituteSecrets(b, mapLookup(map[string]string{"OPENAI_KEY": "sk-abc"}))
+	require.NoError(t, err)
+	assert.Equal(t, "sk-abc", b.Profile.Upstreams[0].APIKey)
+	assert.Equal(t, "https://api.openai.com", b.Profile.Upstreams[0].BaseURL)
+}
+
+func TestSubstituteSecretsMCPEnv(t *testing.T) {
+	b := &Bundle{
+		MCP: MCPRegistry{
+			Servers: []MCPServer{
+				{Name: "myserver", Env: map[string]string{"API_KEY": "${SRV_KEY}"}},
+			},
+		},
+	}
+	err := SubstituteSecrets(b, mapLookup(map[string]string{"SRV_KEY": "srv-secret"}))
+	require.NoError(t, err)
+	assert.Equal(t, "srv-secret", b.MCP.Servers[0].Env["API_KEY"])
+}
+
+func TestSubstituteSecretsMCPArgs(t *testing.T) {
+	b := &Bundle{
+		MCP: MCPRegistry{
+			Servers: []MCPServer{
+				{Name: "myserver", Args: []string{"--token", "${MCP_TOKEN}", "--plain"}},
+			},
+		},
+	}
+	err := SubstituteSecrets(b, mapLookup(map[string]string{"MCP_TOKEN": "tok"}))
+	require.NoError(t, err)
+	assert.Equal(t, []string{"--token", "tok", "--plain"}, b.MCP.Servers[0].Args)
+}
+
+func TestSubstituteSecretsMissingVarErrors(t *testing.T) {
+	b := &Bundle{
+		Profile: Profile{
+			Name: "test",
+			Gateway: Gateway{
+				Token: "${MISSING_TOKEN}",
+			},
+		},
+	}
+	err := SubstituteSecrets(b, mapLookup(map[string]string{}))
+	require.Error(t, err)
+	assert.Contains(t, err.Error(), "MISSING_TOKEN")
+	assert.Contains(t, err.Error(), "profile.gateway.token")
+}
+
+func TestSubstituteSecretsSkillBodyUntouched(t *testing.T) {
+	b := &Bundle{
+		Profile: Profile{Name: "test"},
+		Skills: []Skill{
+			{Name: "mys", Body: "Use ${FOO} in your prompt."},
+		},
+	}
+	err := SubstituteSecrets(b, mapLookup(map[string]string{}))
+	require.NoError(t, err)
+	// skill body must be unchanged — ${FOO} is content, not config
+	assert.Equal(t, "Use ${FOO} in your prompt.", b.Skills[0].Body)
+}
diff --git a/internal/canonical/testdata/malformed_config/config.yaml b/internal/canonical/testdata/malformed_config/config.yaml
new file mode 100644
index 0000000..18e9a55
--- /dev/null
+++ b/internal/canonical/testdata/malformed_config/config.yaml
@@ -0,0 +1 @@
+active_profile: [bad yaml: {
diff --git a/internal/canonical/testdata/missing_active_profile/config.yaml b/internal/canonical/testdata/missing_active_profile/config.yaml
new file mode 100644
index 0000000..99ad89e
--- /dev/null
+++ b/internal/canonical/testdata/missing_active_profile/config.yaml
@@ -0,0 +1,2 @@
+enabled_harnesses: [claude-code]
+active_profile: nonexistent
diff --git a/internal/canonical/testdata/profile_no_name/config.yaml b/internal/canonical/testdata/profile_no_name/config.yaml
new file mode 100644
index 0000000..32eb27d
--- /dev/null
+++ b/internal/canonical/testdata/profile_no_name/config.yaml
@@ -0,0 +1,2 @@
+enabled_harnesses: [claude-code]
+active_profile: noname
diff --git a/internal/canonical/testdata/profile_no_name/profiles/noname.yaml b/internal/canonical/testdata/profile_no_name/profiles/noname.yaml
new file mode 100644
index 0000000..95cdf86
--- /dev/null
+++ b/internal/canonical/testdata/profile_no_name/profiles/noname.yaml
@@ -0,0 +1,5 @@
+gateway:
+  url: https://gw.lan
+  token: dummy
+models:
+  - id: claude-sonnet-4-6
diff --git a/internal/cli/apply.go b/internal/cli/apply.go
index d5485b2..372737f 100644
--- a/internal/cli/apply.go
+++ b/internal/cli/apply.go
@@ -13,13 +13,25 @@ import (
 	"github.com/lukaszraczylo/harness-sync/internal/gitx"
 )
 
+// isTerminal returns true when os.Stdin is an interactive terminal.
+// Used to decide whether to show the first-run prompt.
+func isTerminal() bool {
+	fi, err := os.Stdin.Stat()
+	if err != nil {
+		return false
+	}
+	return (fi.Mode() & os.ModeCharDevice) != 0
+}
+
 // NewApply returns the `apply` subcommand. It renders the canonical bundle
 // to each detected (or selected) harness using the apply pipeline.
 func NewApply(reg *adapter.Registry) *cobra.Command {
 	var (
-		dryRun bool
-		force  bool
-		root   string
+		dryRun          bool
+		force           bool
+		root            string
+		allowIncomplete bool
+		yes             bool
 	)
 	cmd := &cobra.Command{
 		Use:   "apply [harness...]",
@@ -37,6 +49,31 @@ func NewApply(reg *adapter.Registry) *cobra.Command {
 				return err
 			}
 
+			// Issue 3: refuse apply when gateway is incomplete.
+			if !allowIncomplete && (b.Profile.Gateway.URL == "" || b.Profile.Gateway.DefaultModel == "") {
+				return fmt.Errorf("profile %q is incomplete (gateway.url or gateway.default_model is empty); edit %s/profiles/%s.yaml then re-run",
+					b.Profile.Name, root, b.Profile.Name)
+			}
+
+			// Issue 5: first-time apply warning (state/ doesn't exist yet).
+			if !dryRun {
+				statePath := filepath.Join(root, "state")
+				if _, statErr := os.Stat(statePath); os.IsNotExist(statErr) {
+					if !yes && isTerminal() {
+						_, _ = fmt.Fprintf(cmd.OutOrStdout(),
+							"First-time apply to detected harnesses. harness-sync will:\n"+
+								"  - move existing target files to %s/backups/<harness>/\n"+
+								"  - replace them with symlinks to %s/skills, %s/agents\n"+
+								"  - render LLM configs from the active profile\n\n"+
+								"Continue? [y/N] ", root, root, root)
+						var answer string
+						if _, scanErr := fmt.Fscan(cmd.InOrStdin(), &answer); scanErr != nil || (answer != "y" && answer != "Y") {
+							return fmt.Errorf("aborted")
+						}
+					}
+				}
+			}
+
 			var selected []adapter.Adapter
 			if len(args) == 0 {
 				for _, a := range reg.All() {
@@ -87,5 +124,7 @@ func NewApply(reg *adapter.Registry) *cobra.Command {
 	cmd.Flags().BoolVar(&dryRun, "dry-run", false, "print actions without writing")
 	cmd.Flags().BoolVar(&force, "force", false, "overwrite without 3-way merge")
 	cmd.Flags().StringVar(&root, "root", "", "canonical root (default ~/.config/harness-sync)")
+	cmd.Flags().BoolVar(&allowIncomplete, "allow-incomplete", false, "apply even when gateway.url or gateway.default_model is empty (for testing)")
+	cmd.Flags().BoolVar(&yes, "yes", false, "skip first-run confirmation prompt")
 	return cmd
 }
diff --git a/internal/cli/apply_test.go b/internal/cli/apply_test.go
index 055c3af..a801d5b 100644
--- a/internal/cli/apply_test.go
+++ b/internal/cli/apply_test.go
@@ -30,3 +30,43 @@ func TestApplyDryRun(t *testing.T) {
 
 	assert.Contains(t, buf.String(), "dry-run")
 }
+
+// TestApplyRefusesIncompleteProfile: apply must error when gateway.url or
+// gateway.default_model is empty.
+func TestApplyRefusesIncompleteProfile(t *testing.T) {
+	root := t.TempDir()
+	require.NoError(t, os.WriteFile(filepath.Join(root, "config.yaml"), []byte("active_profile: bad\n"), 0o600))
+	require.NoError(t, os.MkdirAll(filepath.Join(root, "profiles"), 0o750))
+	// Profile with empty url and default_model.
+	require.NoError(t, os.WriteFile(filepath.Join(root, "profiles", "bad.yaml"),
+		[]byte("name: bad\ngateway:\n  url: \"\"\n  token: dummy\n  default_model: \"\"\nmodels: []\n"), 0o600))
+
+	reg := adapter.NewRegistry()
+	reg.Register(&detectableAdapter{name: "stub", detect: true})
+
+	cmd := NewApply(reg)
+	cmd.SetArgs([]string{"--root", root})
+	err := cmd.Execute()
+	require.Error(t, err)
+	assert.Contains(t, err.Error(), "incomplete")
+}
+
+// TestApplyAllowIncompleteFlag: --allow-incomplete bypasses the gateway check.
+func TestApplyAllowIncompleteFlag(t *testing.T) {
+	root := t.TempDir()
+	require.NoError(t, os.WriteFile(filepath.Join(root, "config.yaml"), []byte("active_profile: bad\n"), 0o600))
+	require.NoError(t, os.MkdirAll(filepath.Join(root, "profiles"), 0o750))
+	require.NoError(t, os.WriteFile(filepath.Join(root, "profiles", "bad.yaml"),
+		[]byte("name: bad\ngateway:\n  url: \"\"\n  token: dummy\n  default_model: \"\"\nmodels: []\n"), 0o600))
+
+	reg := adapter.NewRegistry()
+	reg.Register(&detectableAdapter{name: "stub", detect: true})
+
+	var buf bytes.Buffer
+	cmd := NewApply(reg)
+	cmd.SetOut(&buf)
+	// --yes skips first-run prompt; --allow-incomplete skips gateway check.
+	cmd.SetArgs([]string{"--root", root, "--dry-run", "--allow-incomplete", "--yes"})
+	require.NoError(t, cmd.Execute())
+	assert.Contains(t, buf.String(), "dry-run")
+}
diff --git a/internal/cli/diff.go b/internal/cli/diff.go
index fc1dff8..a12a125 100644
--- a/internal/cli/diff.go
+++ b/internal/cli/diff.go
@@ -17,7 +17,7 @@ func NewDiff(reg *adapter.Registry) *cobra.Command {
 			apply := NewApply(reg)
 			apply.SetOut(cmd.OutOrStdout())
 			apply.SetErr(cmd.ErrOrStderr())
-			applyArgs := []string{"--dry-run"}
+			applyArgs := []string{"--dry-run", "--allow-incomplete"}
 			if root != "" {
 				applyArgs = append(applyArgs, "--root", root)
 			}
diff --git a/internal/cli/init.go b/internal/cli/init.go
index 257fbdc..1124751 100644
--- a/internal/cli/init.go
+++ b/internal/cli/init.go
@@ -23,6 +23,7 @@ func NewInit(reg *adapter.Registry) *cobra.Command {
 		home     string
 		from     []string
 		noPrompt bool
+		force    bool
 	)
 	cmd := &cobra.Command{
 		Use:   "init",
@@ -42,6 +43,10 @@ func NewInit(reg *adapter.Registry) *cobra.Command {
 			if err = os.MkdirAll(r, 0o750); err != nil {
 				return err
 			}
+			// Issue 1: refuse overwrite without --force
+			if _, statErr := os.Stat(filepath.Join(r, "config.yaml")); statErr == nil && !force {
+				return fmt.Errorf("canonical root %s already initialised (use --force to re-import; existing skills/agents/mcp will be merged)", r)
+			}
 			candidates := reg.DetectedNames()
 			if len(candidates) == 0 {
 				return fmt.Errorf("no harnesses detected under %s", home)
@@ -77,6 +82,7 @@ func NewInit(reg *adapter.Registry) *cobra.Command {
 	cmd.Flags().StringVar(&home, "home", "", "home dir (default $HOME)")
 	cmd.Flags().StringSliceVar(&from, "from", nil, "import from specific adapter(s), skip prompt")
 	cmd.Flags().BoolVar(&noPrompt, "no-prompt", false, "import from all detected adapters without prompting")
+	cmd.Flags().BoolVar(&force, "force", false, "re-import even if canonical root already initialised")
 	return cmd
 }
 
@@ -153,6 +159,18 @@ func runImport(cmd *cobra.Command, reg *adapter.Registry, root, home string, pic
 	return nil
 }
 
+// importedProfileBody is the placeholder written to profiles/imported.yaml on first init.
+// Written using escape sequences to avoid literal newlines in string literals.
+const importedProfileBody = "# harness-sync profile \xe2\x80\x94 generated by init\n" +
+	"# Edit the gateway block below to point at your LLM gateway before running\n" +
+	"# `harness-sync apply`. The dummy token is fine for most local gateways.\n" +
+	"name: imported\n" +
+	"gateway:\n" +
+	"  url: \"\"                              # \xe2\x86\x90 set this\n" +
+	"  token: \"dummy\"\n" +
+	"  default_model: \"\"                    # \xe2\x86\x90 set this\n" +
+	"models: []\n"
+
 func writeCanonical(root string, b *canonical.Bundle, picked []string) error {
 	for _, sub := range []string{"profiles", "skills", "agents", "instructions"} {
 		if err := os.MkdirAll(filepath.Join(root, sub), 0o750); err != nil {
@@ -171,20 +189,12 @@ func writeCanonical(root string, b *canonical.Bundle, picked []string) error {
 		return err
 	}
 
-	profBody, err := render.YAML(canonical.Profile{
-		Name: "imported",
-		Gateway: canonical.Gateway{
-			URL:          "https://gateway.local",
-			Token:        "dummy",
-			DefaultModel: "claude-sonnet-4-6",
-		},
-		Models: []canonical.Model{{ID: "claude-sonnet-4-6", Alias: "sonnet"}},
-	})
-	if err != nil {
-		return err
-	}
-	if err = os.WriteFile(filepath.Join(root, "profiles", "imported.yaml"), profBody, 0o600); err != nil {
-		return err
+	// Issue 2: write placeholder profile only if it doesn't exist yet (preserve user edits on re-init).
+	profPath := filepath.Join(root, "profiles", "imported.yaml")
+	if _, statErr := os.Stat(profPath); os.IsNotExist(statErr) {
+		if err = os.WriteFile(profPath, []byte(importedProfileBody), 0o600); err != nil {
+			return err
+		}
 	}
 
 	if len(b.MCP.Servers) > 0 {
diff --git a/internal/cli/init_test.go b/internal/cli/init_test.go
index 7006b6a..73d6309 100644
--- a/internal/cli/init_test.go
+++ b/internal/cli/init_test.go
@@ -49,3 +49,57 @@ func TestInitImportWritesCanonical(t *testing.T) {
 	_, err := os.Stat(filepath.Join(root, ".git"))
 	require.NoError(t, err)
 }
+
+func makeStubReg() *adapter.Registry {
+	reg := adapter.NewRegistry()
+	reg.Register(&importableAdapter{
+		name: "stub",
+		res:  &adapter.ImportResult{},
+	})
+	return reg
+}
+
+// TestInitRefusesOverwriteWithoutForce: second init without --force must error.
+func TestInitRefusesOverwriteWithoutForce(t *testing.T) {
+	root := t.TempDir()
+	home := t.TempDir()
+
+	// First init — should succeed.
+	cmd := NewInit(makeStubReg())
+	cmd.SetArgs([]string{"--root", root, "--home", home, "--from", "stub", "--no-prompt"})
+	require.NoError(t, cmd.Execute())
+
+	// Second init — must fail without --force.
+	cmd2 := NewInit(makeStubReg())
+	cmd2.SetArgs([]string{"--root", root, "--home", home, "--from", "stub", "--no-prompt"})
+	err := cmd2.Execute()
+	require.Error(t, err)
+	assert.Contains(t, err.Error(), "already initialised")
+	assert.Contains(t, err.Error(), "--force")
+}
+
+// TestInitForcePreservesExistingProfile: --force re-imports but does NOT overwrite imported.yaml.
+func TestInitForcePreservesExistingProfile(t *testing.T) {
+	root := t.TempDir()
+	home := t.TempDir()
+
+	// First init writes placeholder profile.
+	cmd := NewInit(makeStubReg())
+	cmd.SetArgs([]string{"--root", root, "--home", home, "--from", "stub", "--no-prompt"})
+	require.NoError(t, cmd.Execute())
+
+	// User edits the profile.
+	profPath := filepath.Join(root, "profiles", "imported.yaml")
+	userEdit := []byte("name: imported\ngateway:\n  url: \"https://my.gateway\"\n  token: \"tok\"\n  default_model: \"m\"\nmodels: []\n")
+	require.NoError(t, os.WriteFile(profPath, userEdit, 0o600))
+
+	// Re-init with --force.
+	cmd2 := NewInit(makeStubReg())
+	cmd2.SetArgs([]string{"--root", root, "--home", home, "--from", "stub", "--no-prompt", "--force"})
+	require.NoError(t, cmd2.Execute())
+
+	// User edits must be preserved.
+	got, err := os.ReadFile(profPath)
+	require.NoError(t, err)
+	assert.Equal(t, string(userEdit), string(got))
+}
diff --git a/internal/cli/profile.go b/internal/cli/profile.go
index 5fcadb8..47e5193 100644
--- a/internal/cli/profile.go
+++ b/internal/cli/profile.go
@@ -8,10 +8,13 @@ import (
 	"strings"
 
 	"github.com/spf13/cobra"
+
+	"github.com/lukaszraczylo/harness-sync/internal/adapter"
 )
 
 // NewProfile returns the `profile` subcommand with `list` and `use`.
-func NewProfile() *cobra.Command {
+// reg is used by the `use --apply` flag to invoke apply after switching.
+func NewProfile(reg *adapter.Registry) *cobra.Command {
 	var root string
 	rootFlag := func(c *cobra.Command) {
 		c.Flags().StringVar(&root, "root", "", "canonical root (default ~/.config/harness-sync)")
@@ -44,6 +47,7 @@ func NewProfile() *cobra.Command {
 	}
 	rootFlag(list)
 
+	var applyAfter bool
 	use := &cobra.Command{
 		Use:   "use <name>",
 		Short: "Set active profile (rewrites config.yaml)",
@@ -61,10 +65,24 @@ func NewProfile() *cobra.Command {
 			configPath := filepath.Join(r, "config.yaml")
 			existing, _ := os.ReadFile(configPath)
 			updated := setActiveProfile(string(existing), target)
-			return os.WriteFile(configPath, []byte(updated), 0o600)
+			if err := os.WriteFile(configPath, []byte(updated), 0o600); err != nil {
+				return err
+			}
+			_, _ = fmt.Fprintf(cmd.OutOrStdout(),
+				"Switched active profile to %q. Run `harness-sync apply` to propagate.\n", target)
+			// Issue 4: --apply flag auto-invokes apply after switching.
+			if applyAfter {
+				applyCmd := NewApply(reg)
+				applyCmd.SetOut(cmd.OutOrStdout())
+				applyCmd.SetErr(cmd.ErrOrStderr())
+				applyCmd.SetArgs([]string{"--root", r, "--yes"})
+				return applyCmd.Execute()
+			}
+			return nil
 		},
 	}
 	rootFlag(use)
+	use.Flags().BoolVar(&applyAfter, "apply", false, "run apply automatically after switching profile")
 
 	cmd := &cobra.Command{Use: "profile", Short: "Manage profiles"}
 	cmd.AddCommand(list, use)
diff --git a/internal/cli/profile_test.go b/internal/cli/profile_test.go
index 4602a23..79ca72e 100644
--- a/internal/cli/profile_test.go
+++ b/internal/cli/profile_test.go
@@ -4,10 +4,13 @@ import (
 	"bytes"
 	"os"
 	"path/filepath"
+	"strings"
 	"testing"
 
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
+
+	"github.com/lukaszraczylo/harness-sync/internal/adapter"
 )
 
 func TestProfileList(t *testing.T) {
@@ -17,7 +20,7 @@ func TestProfileList(t *testing.T) {
 	require.NoError(t, os.WriteFile(filepath.Join(root, "profiles", "work.yaml"), []byte("name: work\n"), 0o600))
 
 	var buf bytes.Buffer
-	cmd := NewProfile()
+	cmd := NewProfile(nil)
 	cmd.SetArgs([]string{"list", "--root", root})
 	cmd.SetOut(&buf)
 	require.NoError(t, cmd.Execute())
@@ -33,7 +36,7 @@ func TestProfileUse(t *testing.T) {
 	require.NoError(t, os.WriteFile(filepath.Join(root, "profiles", "work.yaml"), []byte("name: work\n"), 0o600))
 	require.NoError(t, os.WriteFile(filepath.Join(root, "config.yaml"), []byte("active_profile: home\n"), 0o600))
 
-	cmd := NewProfile()
+	cmd := NewProfile(nil)
 	cmd.SetArgs([]string{"use", "work", "--root", root})
 	require.NoError(t, cmd.Execute())
 
@@ -41,3 +44,52 @@ func TestProfileUse(t *testing.T) {
 	require.NoError(t, err)
 	assert.Contains(t, string(body), "active_profile: work")
 }
+
+// TestProfileUseHintMessage verifies the "run apply" hint is printed.
+func TestProfileUseHintMessage(t *testing.T) {
+	root := t.TempDir()
+	require.NoError(t, os.MkdirAll(filepath.Join(root, "profiles"), 0o750))
+	require.NoError(t, os.WriteFile(filepath.Join(root, "profiles", "work.yaml"), []byte("name: work\n"), 0o600))
+	require.NoError(t, os.WriteFile(filepath.Join(root, "config.yaml"), []byte("active_profile: home\n"), 0o600))
+
+	var buf bytes.Buffer
+	cmd := NewProfile(nil)
+	cmd.SetOut(&buf)
+	cmd.SetArgs([]string{"use", "work", "--root", root})
+	require.NoError(t, cmd.Execute())
+
+	assert.Contains(t, buf.String(), "Switched active profile to")
+	assert.Contains(t, buf.String(), "harness-sync apply")
+}
+
+// TestProfileUseWithApply verifies --apply triggers apply after switching.
+func TestProfileUseWithApply(t *testing.T) {
+	root := t.TempDir()
+	require.NoError(t, os.MkdirAll(filepath.Join(root, "profiles"), 0o750))
+	// Profile must be complete so apply doesn't refuse.
+	profYAML := "name: work\ngateway:\n  url: https://gw\n  token: tok\n  default_model: m\nmodels:\n  - {id: m}\n"
+	require.NoError(t, os.WriteFile(filepath.Join(root, "profiles", "work.yaml"), []byte(profYAML), 0o600))
+	require.NoError(t, os.WriteFile(filepath.Join(root, "config.yaml"), []byte("active_profile: home\n"), 0o600))
+
+	reg := adapter.NewRegistry()
+	// No adapters detected → apply runs but writes 0 files (nothing to render).
+	reg.Register(&detectableAdapter{name: "stub", detect: false})
+
+	var buf bytes.Buffer
+	cmd := NewProfile(reg)
+	cmd.SetOut(&buf)
+	// --yes bypasses first-run prompt in apply; state/ won't exist.
+	cmd.SetArgs([]string{"use", "work", "--root", root, "--apply"})
+	require.NoError(t, cmd.Execute())
+
+	out := buf.String()
+	assert.Contains(t, out, "Switched active profile")
+	// apply output: "applied: 0 written ..."
+	assert.True(t, strings.Contains(out, "applied") || strings.Contains(out, "dry-run"),
+		"expected apply output in: %s", out)
+
+	// config.yaml must now reference work.
+	body, err := os.ReadFile(filepath.Join(root, "config.yaml"))
+	require.NoError(t, err)
+	assert.Contains(t, string(body), "active_profile: work")
+}
diff --git a/tests/e2e/e2e_test.go b/tests/e2e/e2e_test.go
index 691499f..f8370b6 100644
--- a/tests/e2e/e2e_test.go
+++ b/tests/e2e/e2e_test.go
@@ -37,7 +37,9 @@ func TestInitApplyDiffCycle(t *testing.T) {
 	// apply may produce conflicts on a freshly imported tree (because the
 	// claude-code adapter merges into existing settings.json which differs
 	// from canonical); accept either clean exit or conflict exit.
-	out, err = run("apply")
+	// --allow-incomplete: the placeholder profile has empty URL by design.
+	// --yes: skip first-run TTY prompt in CI.
+	out, err = run("apply", "--allow-incomplete", "--yes")
 	if err != nil {
 		// Apply with conflicts is acceptable — verify the binary at least ran
 		assert.Contains(t, string(out), "applied")