refactor(config): isolate global MCP and skills config / 重构配置：隔离全局 MCP 和 Skills 配置

README.md

@@ -179,6 +179,11 @@ url     = "https://mcp.stripe.com"
 headers = { Authorization = "Bearer ${STRIPE_KEY}" }
 ```
 
+Enabled MCP servers start connecting automatically in the background after a
+session begins, so chat stays usable while tools come online. Use `/mcp` or the
+desktop MCP panel to refresh status, reconnect a server, inspect failures, or
+disable a server for the current session.
+
 **Already have an `.mcp.json`?** Drop it in the project root and Reasonix
 reads it as-is — the `mcpServers` spec (`command`/`args`/`env`, `type`/`url`/
 `headers`, `${VAR}` expansion) maps field-for-field onto `[[plugins]]`. Both

desktop/app.go

@@ -1467,14 +1467,17 @@ func skillRootsView() []SkillRootView {
 	cfg, _ := config.Load()
 	userCfg := config.LoadForEdit(config.UserConfigPath())
 	var custom []string
+	maxDepth := 3
 	if cfg != nil {
 		custom = cfg.SkillCustomPaths()
+		maxDepth = cfg.SkillMaxDepth()
 	}
-	st := skill.New(skill.Options{ProjectRoot: cwd, CustomPaths: custom, DisableBuiltins: true, Stderr: io.Discard})
+	st := skill.New(skill.Options{ProjectRoot: cwd, CustomPaths: custom, MaxDepth: maxDepth, DisableBuiltins: true, Stderr: io.Discard})
 	counts := map[string]int{}
 	skillItems := map[string][]SkillRootSkillView{}
+	roots := st.Roots()
 	for _, sk := range st.List() {
-		root := config.CanonicalSkillPath(filepath.Dir(skillRootPath(sk.Path)))
+		root := skillDisplayRoot(sk, roots)
 		counts[root]++
 		skillItems[root] = append(skillItems[root], SkillRootSkillView{
 			Name:        sk.Name,
@@ -1495,7 +1498,7 @@ func skillRootsView() []SkillRootView {
 		}
 	}
 	out := []SkillRootView{}
-	for _, r := range st.Roots() {
+	for _, r := range roots {
 		dir := config.CanonicalSkillPath(r.Dir)
 		view := SkillRootView{
 			Dir:        r.Dir,
@@ -1626,6 +1629,21 @@ func skillRootPath(path string) string {
 	return path
 }
 
+func skillDisplayRoot(sk skill.Skill, roots []skill.Root) string {
+	cleanPath := filepath.Clean(sk.Path)
+	for _, r := range roots {
+		if r.Scope != sk.Scope {
+			continue
+		}
+		cleanRoot := filepath.Clean(r.Dir)
+		prefix := cleanRoot + string(filepath.Separator)
+		if cleanPath == cleanRoot || strings.HasPrefix(cleanPath, prefix) {
+			return config.CanonicalSkillPath(r.Dir)
+		}
+	}
+	return config.CanonicalSkillPath(filepath.Dir(skillRootPath(sk.Path)))
+}
+
 // MCPServerInput is the drawer's "add server" form. Transport is "stdio" (Command
 // + Args + Env) or "http"/"sse" (URL). Mirrors config.PluginEntry's writable shape.
 type MCPServerInput struct {
@@ -1635,7 +1653,6 @@ type MCPServerInput struct {
 	Args      []string          `json:"args"`
 	URL       string            `json:"url"`
 	Env       map[string]string `json:"env"`
-	Tier      string            `json:"tier"`
 }
 
 // AddMCPServer connects a server live and persists it to config (Customize → MCP →
@@ -1652,8 +1669,8 @@ func (a *App) AddMCPServer(in MCPServerInput) (int, error) {
 		Args:    in.Args,
 		URL:     in.URL,
 		Env:     in.Env,
-		Tier:    normalizeMCPTier(in.Tier),
 	}
+	entry, _ = config.NormalizePluginCommandLine(entry)
 	if err := a.saveDesktopMCPServer(entry); err != nil {
 		return 0, err
 	}
@@ -1684,10 +1701,11 @@ func (a *App) UpdateMCPServer(name string, in MCPServerInput) error {
 	updated.Command = strings.TrimSpace(in.Command)
 	updated.Args = append([]string(nil), in.Args...)
 	updated.URL = strings.TrimSpace(in.URL)
-	updated.Tier = normalizeMCPTier(in.Tier)
+	updated.Tier = ""
 	if in.Env != nil {
 		updated.Env = in.Env
 	}
+	updated, _ = config.NormalizePluginCommandLine(updated)
 	if updated.Type == "stdio" {
 		updated.URL = ""
 	} else {
@@ -1743,15 +1761,26 @@ func (a *App) RemoveMCPServer(name string) error {
 	return fmt.Errorf("no MCP server named %q", name)
 }
 
-// RetryMCPServer reconnects a configured server that failed or was disconnected,
-// without touching config (the failed row's retry button).
-func (a *App) RetryMCPServer(name string) error {
+// ReconnectMCPServer disconnects the server if it is already connected (to force
+// a fresh handshake and tool re-registration), then reconnects.  Failures are
+// recorded on the Host so the UI can render them.
+func (a *App) ReconnectMCPServer(name string) error {
 	tab := a.activeTab()
 	if tab == nil || tab.Ctrl == nil {
 		return fmt.Errorf("no active session")
 	}
+	if mcpConnected(tab.Ctrl, name) {
+		tab.Ctrl.DisconnectMCPServer(name)
+	}
 	_, err := a.connectConfiguredMCPServerForTab(tab, name)
-	return err
+	if err != nil {
+		recordMCPFailure(tab.Ctrl, config.PluginEntry{Name: name}, err)
+		return err
+	}
+	a.mu.Lock()
+	delete(tab.disabledMCP, name)
+	a.mu.Unlock()
+	return nil
 }
 
 // ClearMCPServerAuthentication removes local auth-like config for one MCP and
@@ -1829,9 +1858,9 @@ func (a *App) connectConfiguredMCPServerForTab(tab *WorkspaceTab, name string) (
 	return 0, fmt.Errorf("no configured MCP server named %q", name)
 }
 
-// SetMCPServerTier persists how a configured MCP server should start on future
-// sessions. It does not tear down a connected server; the per-session toggle and
-// "connect now" remain separate controls.
+// SetMCPServerTier is kept for old desktop bindings. New config writes drop the
+// retired tier field, so this only affects the active session before the next
+// config reload.
 func (a *App) SetMCPServerTier(name, tier string) error {
 	if name == "codegraph" {
 		return a.setCodegraphTier(tier)
@@ -1878,9 +1907,6 @@ func (a *App) setCodegraphEnabled(enabled bool) error {
 	if err := cfg.SaveTo(path); err != nil {
 		return err
 	}
-	if err := a.syncProjectCodegraphOverride(cfg.Codegraph); err != nil {
-		return err
-	}
 	if enabled {
 		a.mu.Lock()
 		delete(tab.disabledMCP, "codegraph")
@@ -1917,9 +1943,6 @@ func (a *App) setCodegraphTier(tier string) error {
 	if err := cfg.SaveTo(path); err != nil {
 		return err
 	}
-	if err := a.syncProjectCodegraphOverride(cfg.Codegraph); err != nil {
-		return err
-	}
 	tab := a.activeTab()
 	if tab == nil || tab.Ctrl == nil {
 		return nil
@@ -1953,37 +1976,21 @@ func (a *App) desktopMCPServerForEdit(name string) (config.PluginEntry, bool, er
 }
 
 func (a *App) saveDesktopMCPServer(entry config.PluginEntry) error {
-	cfg, path, err := a.loadDesktopUserConfigForEdit()
-	if err != nil {
+	if err := config.UpsertMCPPlugin(entry); err != nil {
 		return err
 	}
-	if err := cfg.UpsertPlugin(entry); err != nil {
-		return err
-	}
-	if err := cfg.SaveTo(path); err != nil {
-		return err
-	}
-	_, err = a.removeProjectMCPOverride(entry.Name)
-	return err
+	// Project-level overrides are no longer supported; clean up legacy entries.
+	_, _ = a.removeProjectMCPOverride(entry.Name)
+	return nil
 }
 
 func (a *App) removeDesktopMCPServer(name string) (bool, error) {
-	removed := false
-	cfg, path, err := a.loadDesktopUserConfigForEdit()
+	found, err := config.RemoveMCPPlugin(name)
 	if err != nil {
 		return false, err
 	}
-	if cfg.RemovePlugin(name) {
-		removed = true
-		if err := cfg.SaveTo(path); err != nil {
-			return false, err
-		}
-	}
-	projectRemoved, err := a.removeProjectMCPOverride(name)
-	if err != nil {
-		return removed, err
-	}
-	return removed || projectRemoved, nil
+	projectRemoved, _ := a.removeProjectMCPOverride(name)
+	return found || projectRemoved, nil
 }
 
 func (a *App) removeProjectMCPOverride(name string) (bool, error) {
@@ -2008,23 +2015,6 @@ func (a *App) removeProjectMCPOverride(name string) (bool, error) {
 	return true, nil
 }
 
-func (a *App) syncProjectCodegraphOverride(c config.CodegraphConfig) error {
-	path := projectConfigPathForRoot(a.activeWorkspaceRoot())
-	userPath := config.UserConfigPath()
-	if path == "" || sameConfigPath(path, userPath) {
-		return nil
-	}
-	if _, err := os.Stat(path); err != nil {
-		if os.IsNotExist(err) {
-			return nil
-		}
-		return err
-	}
-	cfg := config.LoadForEdit(path)
-	cfg.Codegraph = c
-	return cfg.SaveTo(path)
-}
-
 func findPluginEntry(entries []config.PluginEntry, name string) (config.PluginEntry, bool) {
 	for _, p := range entries {
 		if p.Name == name {
@@ -2040,6 +2030,8 @@ func normalizeMCPTier(tier string) string {
 		return "eager"
 	case "background":
 		return "background"
+	case "":
+		return "background"
 	default:
 		return "lazy"
 	}