refactor: split preferences into user and org scopes

Split the monolithic Preferences service into UserPreferences (env-level)
and OrgPreferences (org-level). User preferences (theme, active org, role)
persist across org switches. Org preferences (account, workspace) are
scoped to each organization.

- Add theme preference (auto/dark/light) with auto-detection default
- Rename config.yaml to preferences.yaml at both scopes
- Absorb active.yaml into user-level preferences.yaml
- Use typed domain IDs (OrganizationID, AccountID, WorkspaceID) in config
- Remove dead preference fields (Services, Email, DatadogAPIKey, etc.)
- Extract migration logic into migrate.go with detect-and-dispatch pattern
- Add migration tests covering all prior disk layouts (V1/V2/V3)
- Replace map[string]interface{} with map[string]any

Author: binarylogic

internal/app/app.go

@@ -70,7 +70,8 @@ type Model struct {
 	authService auth.Auth
 	syncer      powersync.Syncer
 	services    api.APIServices
-	prefs       preferences.Preferences
+	userPrefs   preferences.UserPreferences
+	orgPrefs    preferences.OrgPreferences
 
 	// Runtime (created after account selection / onboarding)
 	sessionCancel context.CancelFunc
@@ -108,7 +109,8 @@ func New(
 	version string,
 	services api.APIServices,
 	authService auth.Auth,
-	prefs preferences.Preferences,
+	userPrefs preferences.UserPreferences,
+	orgPrefs preferences.OrgPreferences,
 	storage sqlite.Storage,
 	syncer powersync.Syncer,
 	scope log.Scope,
@@ -122,8 +124,11 @@ func New(
 	if authService == nil {
 		panic("authService is nil")
 	}
-	if prefs == nil {
-		panic("prefs is nil")
+	if userPrefs == nil {
+		panic("userPrefs is nil")
+	}
+	if orgPrefs == nil {
+		panic("orgPrefs is nil")
 	}
 	if storage == nil {
 		panic("storage is nil")
@@ -144,11 +149,12 @@ func New(
 		authService: authService,
 		syncer:      syncer,
 		services:    services,
-		prefs:       prefs,
+		userPrefs:   userPrefs,
+		orgPrefs:    orgPrefs,
 		statusBar:   statusbar.New(theme, syncer, cfg.APIEndpoint),
 		toast:       toast.New(theme),
 		keyBar:      keybar.New(theme, scope),
-		onboarding:  onboarding.New(ctx, theme, services, prefs, authService, syncer, scope),
+		onboarding:  onboarding.New(ctx, theme, services, userPrefs, orgPrefs, authService, syncer, scope),
 		state:       stateOnboarding,
 	}
 }
@@ -259,10 +265,10 @@ func (m *Model) Update(msg tea.Msg) (tea.Model, tea.Cmd) {
 		}
 
 	case onboardingmsg.OrgSelected:
-		return m, m.activateOrg(msg.Org.ID.String(), msg)
+		return m, m.activateOrg(msg.Org.ID, msg)
 
 	case onboardingmsg.OrgCreated:
-		return m, m.activateOrg(msg.Org.ID.String(), msg)
+		return m, m.activateOrg(msg.Org.ID, msg)
 
 	case onboardingmsg.AccountSelected:
 		// Open database and start syncer when account is selected
@@ -708,21 +714,21 @@ func (m *Model) shutdown() {
 	}
 }
 
-// activateOrg sets the active org, reloads config/prefs/storage for the new
+// activateOrg sets the active org, reloads org prefs/storage for the new
 // org's isolated data directory, and forwards the message to onboarding.
-func (m *Model) activateOrg(orgID string, msg tea.Msg) tea.Cmd {
+func (m *Model) activateOrg(orgID domain.OrganizationID, msg tea.Msg) tea.Cmd {
 	env := m.cfg.Environment()
 	m.scope.Info("setting active org", "org_id", orgID)
-	_ = config.SetActiveOrgID(env, orgID)
+	_ = m.userPrefs.SetActiveOrgID(orgID)
 
-	cfg, err := config.Load(env, orgID)
+	cfg, err := config.LoadOrgPreferences(env, orgID)
 	if err != nil {
 		m.scope.Error("failed to reload config for org", "error", err)
 	} else {
-		m.prefs = preferences.NewService(cfg, m.scope)
+		m.orgPrefs = preferences.NewOrgService(cfg, m.scope)
 		m.storage = sqlite.NewStorageService(cfg)
 		if m.onboarding != nil {
-			m.onboarding.SetPreferences(m.prefs)
+			m.onboarding.SetOrgPreferences(m.orgPrefs)
 		}
 	}
 
@@ -744,7 +750,7 @@ func (m *Model) switchOrganization() tea.Cmd {
 // re-enters onboarding. The saved org auto-selects, then prompts for account.
 func (m *Model) switchAccount() tea.Cmd {
 	m.scope.Info("switching account")
-	_ = m.prefs.ClearDefaultAccountID()
+	_ = m.orgPrefs.ClearDefaultAccountID()
 	return m.restartOnboarding()
 }
 
@@ -763,7 +769,7 @@ func (m *Model) restartOnboarding() tea.Cmd {
 	m.statusBar = statusbar.New(m.theme, m.syncer, m.cfg.APIEndpoint)
 	m.windowTitle = ""
 
-	m.onboarding = onboarding.New(m.ctx, m.theme, m.services, m.prefs, m.authService, m.syncer, m.scope)
+	m.onboarding = onboarding.New(m.ctx, m.theme, m.services, m.userPrefs, m.orgPrefs, m.authService, m.syncer, m.scope)
 	m.state = stateOnboarding
 	m.updateLayout()
 

internal/app/onboarding/accounts/create.go

@@ -29,7 +29,7 @@ type CreateModel struct {
 	ctx      context.Context
 	theme    styles.Theme
 	services api.APIServices
-	prefs    preferences.Preferences
+	prefs    preferences.OrgPreferences
 	scope    log.Scope
 	org      domain.Organization
 
@@ -46,7 +46,7 @@ func NewCreate(
 	theme styles.Theme,
 	org domain.Organization,
 	services api.APIServices,
-	prefs preferences.Preferences,
+	prefs preferences.OrgPreferences,
 	scope log.Scope,
 ) *CreateModel {
 	if ctx == nil {

internal/app/onboarding/accounts/select.go

@@ -23,7 +23,7 @@ type SelectModel struct {
 	ctx      context.Context
 	theme    styles.Theme
 	services api.APIServices
-	prefs    preferences.Preferences
+	prefs    preferences.OrgPreferences
 	scope    log.Scope
 	org      domain.Organization
 
@@ -39,7 +39,7 @@ func NewSelect(
 	theme styles.Theme,
 	org domain.Organization,
 	services api.APIServices,
-	prefs preferences.Preferences,
+	prefs preferences.OrgPreferences,
 	scope log.Scope,
 ) *SelectModel {
 	if ctx == nil {

internal/app/onboarding/onboarding.go

@@ -29,13 +29,14 @@ import (
 // Model is the onboarding orchestrator.
 type Model struct {
 	// Dependencies available from start
-	ctx      context.Context
-	theme    styles.Theme
-	services api.APIServices
-	prefs    preferences.Preferences
-	auth     iauth.Auth
-	syncer   powersync.Syncer
-	scope    log.Scope
+	ctx       context.Context
+	theme     styles.Theme
+	services  api.APIServices
+	userPrefs preferences.UserPreferences
+	orgPrefs  preferences.OrgPreferences
+	auth      iauth.Auth
+	syncer    powersync.Syncer
+	scope     log.Scope
 
 	// Accumulated state from step completions
 	user      *iauth.User
@@ -56,16 +57,20 @@ func New(
 	ctx context.Context,
 	theme styles.Theme,
 	services api.APIServices,
-	prefs preferences.Preferences,
+	userPrefs preferences.UserPreferences,
+	orgPrefs preferences.OrgPreferences,
 	authService iauth.Auth,
 	syncer powersync.Syncer,
 	scope log.Scope,
 ) *Model {
 	if ctx == nil {
 		panic("ctx is nil")
 	}
-	if prefs == nil {
-		panic("prefs is nil")
+	if userPrefs == nil {
+		panic("userPrefs is nil")
+	}
+	if orgPrefs == nil {
+		panic("orgPrefs is nil")
 	}
 	if authService == nil {
 		panic("authService is nil")
@@ -77,20 +82,21 @@ func New(
 	scope = scope.Child("onboarding")
 
 	return &Model{
-		ctx:      ctx,
-		theme:    theme,
-		services: services,
-		prefs:    prefs,
-		auth:     authService,
-		syncer:   syncer,
-		scope:    scope,
+		ctx:       ctx,
+		theme:     theme,
+		services:  services,
+		userPrefs: userPrefs,
+		orgPrefs:  orgPrefs,
+		auth:      authService,
+		syncer:    syncer,
+		scope:     scope,
 	}
 }
 
-// SetPreferences replaces the preferences used by subsequent onboarding steps.
-// Called by the app when switching to a different org-scoped config.
-func (m *Model) SetPreferences(prefs preferences.Preferences) {
-	m.prefs = prefs
+// SetOrgPreferences replaces the org preferences used by subsequent onboarding steps.
+// Called by the app when switching to a different organization.
+func (m *Model) SetOrgPreferences(prefs preferences.OrgPreferences) {
+	m.orgPrefs = prefs
 }
 
 // Init starts the onboarding flow with auth check.
@@ -105,7 +111,7 @@ func (m *Model) Init() tea.Cmd {
 // for selection instead of auto-selecting.
 func (m *Model) StartFromOrgSelect() tea.Cmd {
 	m.scope.Info("onboarding started from org select")
-	return m.setStep(organizations.NewSelect(m.ctx, m.theme, m.services, m.prefs, m.auth, m.scope))
+	return m.setStep(organizations.NewSelect(m.ctx, m.theme, m.services, m.userPrefs, m.auth, m.scope))
 }
 
 // Update handles messages and orchestrates step transitions.
@@ -125,32 +131,32 @@ func (m *Model) Update(msg tea.Msg) tea.Cmd {
 		if msg.NeedsAuth {
 			return m.setStep(auth.NewAuthenticate(m.ctx, m.theme, m.auth, m.scope))
 		}
-		return m.setStep(role.New(m.theme, m.prefs, m.scope))
+		return m.setStep(role.New(m.theme, m.userPrefs, m.scope))
 
 	case msgs.Authenticated:
 		m.scope.Info("user authenticated", "user_id", msg.User.ID)
 		m.user = &msg.User
-		return m.setStep(role.New(m.theme, m.prefs, m.scope))
+		return m.setStep(role.New(m.theme, m.userPrefs, m.scope))
 
 	// Role messages
 	case msgs.RoleSelected:
 		m.scope.Info("role selected", slog.String("role", msg.Role))
-		return m.setStep(organizations.NewSelect(m.ctx, m.theme, m.services, m.prefs, m.auth, m.scope))
+		return m.setStep(organizations.NewSelect(m.ctx, m.theme, m.services, m.userPrefs, m.auth, m.scope))
 
 	// Organization messages
 	case msgs.OrgSelected:
 		m.scope.Info("organization selected", slog.String("org_id", msg.Org.ID.String()))
 		m.org = &msg.Org
-		return m.setStep(accounts.NewSelect(m.ctx, m.theme, msg.Org, m.services, m.prefs, m.scope))
+		return m.setStep(accounts.NewSelect(m.ctx, m.theme, msg.Org, m.services, m.orgPrefs, m.scope))
 
 	case msgs.NoOrgs:
 		m.scope.Debug("no organizations found")
-		return m.setStep(organizations.NewCreate(m.ctx, m.theme, m.services, m.prefs, m.scope))
+		return m.setStep(organizations.NewCreate(m.ctx, m.theme, m.services, m.userPrefs, m.scope))
 
 	case msgs.OrgCreated:
 		m.scope.Info("organization created", slog.String("org_id", msg.Org.ID.String()))
 		m.org = &msg.Org
-		return m.setStep(accounts.NewSelect(m.ctx, m.theme, msg.Org, m.services, m.prefs, m.scope))
+		return m.setStep(accounts.NewSelect(m.ctx, m.theme, msg.Org, m.services, m.orgPrefs, m.scope))
 
 	// Account messages
 	case msgs.AccountSelected:
@@ -161,7 +167,7 @@ func (m *Model) Update(msg tea.Msg) tea.Cmd {
 
 	case msgs.NoAccounts:
 		m.scope.Debug("no accounts found")
-		return m.setStep(accounts.NewCreate(m.ctx, m.theme, msg.Org, m.services, m.prefs, m.scope))
+		return m.setStep(accounts.NewCreate(m.ctx, m.theme, msg.Org, m.services, m.orgPrefs, m.scope))
 
 	case msgs.AccountCreated:
 		m.scope.Info("account created", slog.String("account_id", msg.Account.ID.String()))
@@ -172,7 +178,7 @@ func (m *Model) Update(msg tea.Msg) tea.Cmd {
 	// Datadog messages
 	case msgs.DatadogReady:
 		m.scope.Debug("datadog ready")
-		return m.setStep(workspaces.NewSelect(m.ctx, m.theme, *m.account, m.services, m.prefs, m.scope))
+		return m.setStep(workspaces.NewSelect(m.ctx, m.theme, *m.account, m.services, m.orgPrefs, m.scope))
 
 	case msgs.DatadogNeeded:
 		m.scope.Debug("datadog setup needed")
@@ -194,7 +200,7 @@ func (m *Model) Update(msg tea.Msg) tea.Cmd {
 
 	case msgs.DatadogDiscoveryComplete:
 		m.scope.Info("datadog discovery complete")
-		return m.setStep(workspaces.NewSelect(m.ctx, m.theme, *m.account, m.services, m.prefs, m.scope))
+		return m.setStep(workspaces.NewSelect(m.ctx, m.theme, *m.account, m.services, m.orgPrefs, m.scope))
 
 	// Workspace messages
 	case msgs.WorkspaceSelected:

internal/app/onboarding/organizations/create.go

@@ -28,7 +28,7 @@ type CreateModel struct {
 	ctx      context.Context
 	theme    styles.Theme
 	services api.APIServices
-	prefs    preferences.Preferences
+	prefs    preferences.UserPreferences
 	scope    log.Scope
 
 	input    *input.Model
@@ -43,7 +43,7 @@ func NewCreate(
 	ctx context.Context,
 	theme styles.Theme,
 	services api.APIServices,
-	prefs preferences.Preferences,
+	prefs preferences.UserPreferences,
 	scope log.Scope,
 ) *CreateModel {
 	if ctx == nil {
@@ -82,7 +82,7 @@ func (m *CreateModel) Update(msg tea.Msg) tea.Cmd {
 			m.err = msg.err
 			return appmsg.ErrorCmd("Failed to create organization", msg.err, false)
 		}
-		_ = m.prefs.SetDefaultOrgID(msg.result.Organization.ID)
+		_ = m.prefs.SetActiveOrgID(msg.result.Organization.ID)
 		org := *msg.result.Organization
 		m.scope.Info("organization created", "id", org.ID, "name", org.Name)
 		return func() tea.Msg { return msgs.OrgCreated{Org: org} }

internal/app/onboarding/organizations/select.go

@@ -30,7 +30,7 @@ type SelectModel struct {
 	ctx      context.Context
 	theme    styles.Theme
 	services api.APIServices
-	prefs    preferences.Preferences
+	prefs    preferences.UserPreferences
 	auth     auth.Auth
 	scope    log.Scope
 
@@ -48,7 +48,7 @@ func NewSelect(
 	ctx context.Context,
 	theme styles.Theme,
 	services api.APIServices,
-	prefs preferences.Preferences,
+	prefs preferences.UserPreferences,
 	authService auth.Auth,
 	scope log.Scope,
 ) *SelectModel {
@@ -123,7 +123,7 @@ func (m *SelectModel) Update(msg tea.Msg) tea.Cmd {
 			return func() tea.Msg { return msgs.NoOrgs{} }
 		}
 
-		prefID := m.prefs.GetDefaultOrgID()
+		prefID := m.prefs.GetActiveOrgID()
 		if prefID != "" {
 			for _, org := range m.orgs {
 				if org.ID == prefID {
@@ -135,7 +135,7 @@ func (m *SelectModel) Update(msg tea.Msg) tea.Cmd {
 
 		if len(m.orgs) == 1 {
 			m.scope.Debug("auto-selected organization (only one)")
-			_ = m.prefs.SetDefaultOrgID(m.orgs[0].ID)
+			_ = m.prefs.SetActiveOrgID(m.orgs[0].ID)
 			return m.selectOrg(m.orgs[0])
 		}
 
@@ -158,7 +158,7 @@ func (m *SelectModel) Update(msg tea.Msg) tea.Cmd {
 		case "enter":
 			if item := m.list.SelectedItem(); item != nil {
 				if org, ok := item.(domain.Organization); ok {
-					_ = m.prefs.SetDefaultOrgID(org.ID)
+					_ = m.prefs.SetActiveOrgID(org.ID)
 					return m.selectOrg(org)
 				}
 			}

internal/app/onboarding/role/select.go

@@ -20,15 +20,15 @@ type savedRoleMsg struct {
 // Model handles role selection.
 type Model struct {
 	theme    styles.Theme
-	prefs    preferences.Preferences
+	prefs    preferences.UserPreferences
 	scope    log.Scope
 	selected int
 	width    int
 	height   int
 }
 
 // New creates a new role selection step.
-func New(theme styles.Theme, prefs preferences.Preferences, scope log.Scope) *Model {
+func New(theme styles.Theme, prefs preferences.UserPreferences, scope log.Scope) *Model {
 	if prefs == nil {
 		panic("prefs is nil")
 	}