diff --git a/internal/setup/claude.go b/internal/setup/claude.go
index d98c293..40f2439 100644
--- a/internal/setup/claude.go
+++ b/internal/setup/claude.go
@@ -79,10 +79,65 @@ func ClaudeWriteHook(configDir, filename string, content []byte) (string, error)
 	return hookPath, nil
 }
 
+// userClaudeConfigDir returns the directory Claude Code treats as user-global
+// configuration: $CLAUDE_CONFIG_DIR when set, otherwise ~/.claude.
+func userClaudeConfigDir() string {
+	if dir := os.Getenv("CLAUDE_CONFIG_DIR"); dir != "" {
+		return dir
+	}
+	home, err := os.UserHomeDir()
+	if err != nil {
+		return ""
+	}
+	return filepath.Join(home, ".claude")
+}
+
+// canonicalPath returns the symlink-resolved absolute form of p, falling back
+// to the lexical absolute path when p does not (yet) exist.
+func canonicalPath(p string) string {
+	abs, err := filepath.Abs(p)
+	if err != nil {
+		return p
+	}
+	if resolved, err := filepath.EvalSymlinks(abs); err == nil {
+		return resolved
+	}
+	return abs
+}
+
+// collidesWithUserConfig reports whether a project-local config dir is in fact
+// Claude Code's user-global config dir — the degenerate case of running a
+// project-local setup with cwd == $HOME, where "./.claude" IS "~/.claude".
+// Relative hook commands written into that file load for every session on the
+// machine but only resolve when the session's working directory is $HOME;
+// the user-global file's contract is absolute paths. Both sides are resolved
+// through symlinks before comparison.
+func collidesWithUserConfig(configDir string) bool {
+	userDir := userClaudeConfigDir()
+	if userDir == "" {
+		return false
+	}
+	return canonicalPath(configDir) == canonicalPath(userDir)
+}
+
 // ClaudeRegisterHooks registers selected hooks in settings.json.
 // Prime (SessionStart) is always registered.
+//
+// When the project-local config dir collides with the user-global one (setup
+// run from $HOME), hook commands are written as absolute paths so they honor
+// the global file's contract and resolve from any session directory.
 func ClaudeRegisterHooks(configDir string, sel HookSelection) (string, error) {
 	hooksDir := filepath.Join(configDir, "hooks", "mnemon")
+	if collidesWithUserConfig(configDir) {
+		abs, err := filepath.Abs(hooksDir)
+		if err != nil {
+			return "", err
+		}
+		hooksDir = abs
+		fmt.Printf("  Note: this project config dir is Claude Code's user-global config (%s);\n"+
+			"        writing absolute hook paths so hooks resolve from any directory.\n"+
+			"        Use --global to make a user-wide install explicit.\n", userClaudeConfigDir())
+	}
 	settingsPath := filepath.Join(configDir, "settings.json")
 	data, err := ReadJSONFile(settingsPath)
 	if err != nil {
diff --git a/internal/setup/claude_test.go b/internal/setup/claude_test.go
index 1021720..b3f2c0a 100644
--- a/internal/setup/claude_test.go
+++ b/internal/setup/claude_test.go
@@ -60,3 +60,102 @@ func TestWritePromptFilesWritesUnderMnemonDataDir(t *testing.T) {
 		}
 	}
 }
+
+func TestCollidesWithUserConfigHomeInstall(t *testing.T) {
+	home := t.TempDir()
+	t.Setenv("HOME", home)
+	t.Setenv("CLAUDE_CONFIG_DIR", "")
+	t.Chdir(home)
+
+	if !collidesWithUserConfig(".claude") {
+		t.Fatal("project-local .claude with cwd == $HOME must collide with ~/.claude")
+	}
+
+	proj := t.TempDir()
+	t.Chdir(proj)
+	if collidesWithUserConfig(".claude") {
+		t.Fatal("genuine project-local install must not collide")
+	}
+}
+
+func TestCollidesWithUserConfigResolvesSymlinks(t *testing.T) {
+	base := t.TempDir()
+	real := filepath.Join(base, "realhome")
+	link := filepath.Join(base, "linkhome")
+	if err := os.MkdirAll(filepath.Join(real, ".claude"), 0755); err != nil {
+		t.Fatal(err)
+	}
+	if err := os.Symlink(real, link); err != nil {
+		t.Fatal(err)
+	}
+	t.Setenv("HOME", link) // $HOME reached via symlink
+	t.Setenv("CLAUDE_CONFIG_DIR", "")
+	t.Chdir(real) // cwd is the physical path
+
+	if !collidesWithUserConfig(".claude") {
+		t.Fatal("symlinked $HOME vs physical cwd must still be detected as a collision")
+	}
+}
+
+func TestCollidesWithUserConfigHonorsClaudeConfigDir(t *testing.T) {
+	home := t.TempDir()
+	relocated := t.TempDir()
+	t.Setenv("HOME", home)
+	t.Setenv("CLAUDE_CONFIG_DIR", relocated)
+	t.Chdir(home)
+
+	// With the user config relocated, ~/.claude is NOT the global file.
+	if collidesWithUserConfig(".claude") {
+		t.Fatal("cwd == $HOME must not collide when CLAUDE_CONFIG_DIR points elsewhere")
+	}
+
+	// But installing into the relocated dir itself is a collision.
+	t.Chdir(filepath.Dir(relocated))
+	if !collidesWithUserConfig(filepath.Base(relocated)) {
+		t.Fatal("install targeting the CLAUDE_CONFIG_DIR dir must collide")
+	}
+}
+
+func TestClaudeRegisterHooksCollisionWritesAbsoluteCommands(t *testing.T) {
+	home := t.TempDir()
+	t.Setenv("HOME", home)
+	t.Setenv("CLAUDE_CONFIG_DIR", "")
+	t.Chdir(home)
+
+	if _, err := ClaudeRegisterHooks(".claude", HookSelection{Remind: true, Nudge: true}); err != nil {
+		t.Fatalf("register: %v", err)
+	}
+	data, err := ReadJSONFile(filepath.Join(home, ".claude", "settings.json"))
+	if err != nil {
+		t.Fatal(err)
+	}
+	hooks := data["hooks"].(map[string]any)
+	for _, ev := range []string{"SessionStart", "UserPromptSubmit", "Stop"} {
+		entry := hooks[ev].([]any)[0].(map[string]any)["hooks"].([]any)[0].(map[string]any)
+		cmd := entry["command"].(string)
+		if !filepath.IsAbs(cmd) {
+			t.Fatalf("%s command must be absolute in the user-global file, got %q", ev, cmd)
+		}
+	}
+}
+
+func TestClaudeRegisterHooksProjectLocalStaysRelative(t *testing.T) {
+	home := t.TempDir()
+	proj := t.TempDir()
+	t.Setenv("HOME", home)
+	t.Setenv("CLAUDE_CONFIG_DIR", "")
+	t.Chdir(proj)
+
+	if _, err := ClaudeRegisterHooks(".claude", HookSelection{}); err != nil {
+		t.Fatalf("register: %v", err)
+	}
+	data, err := ReadJSONFile(filepath.Join(proj, ".claude", "settings.json"))
+	if err != nil {
+		t.Fatal(err)
+	}
+	hooks := data["hooks"].(map[string]any)
+	entry := hooks["SessionStart"].([]any)[0].(map[string]any)["hooks"].([]any)[0].(map[string]any)
+	if cmd := entry["command"].(string); filepath.IsAbs(cmd) {
+		t.Fatalf("genuine project-local install must keep existing relative form, got %q", cmd)
+	}
+}