cmd: add --no-skills, --skill, and --skills-dir CLI flags & config (#55)

* cmd: add --no-skills, --skill, and --skills-dir CLI flags

The pkg/kit Options struct already had full backend support for skills
control (NoSkills, Skills []string, SkillsDir) wired into loadSkills()
in pkg/kit/kit.go, but there were no corresponding CLI flags to drive
them. This commit closes that gap.

Changes in cmd/root.go:

- Add three package-level flag variables alongside the existing
  noExtensionsFlag/extensionPaths group:
    noSkillsFlag bool
    skillsPaths  []string
    skillsDir    string

- Register three persistent cobra flags in init():
    --no-skills        disable skill loading (auto-discovery and explicit)
    --skill <path>     load a skill file or directory (repeatable)
    --skills-dir <dir> override the project-local skills directory
                       used for auto-discovery

- Wire all three into the kitOpts struct literal in runNormalMode()
  so they flow directly into kit.New() -> loadSkills().

No changes to pkg/kit or internal/skills -- the backend was already
complete. No viper binding is needed because kit.go reads these fields
directly from opts rather than from viper (unlike NoExtensions which
uses the viper fallback path).

Example usage:
  kit --no-skills "prompt"
  kit --skill ./my-skill.md --skill ./other-skill.md "prompt"
  kit --skills-dir /path/to/skills "prompt"

Co-authored-by: Claude <claude@anthropic.com>

* docs: document --no-skills, --skill, and --skills-dir CLI flags

Add the three new skills CLI flags to all relevant documentation:

- README.md: add Skills section under Global Flags CLI reference
- www/pages/cli/flags.md: add Skills table (mirrors Extensions section pattern)
- www/pages/cli/commands.md: expand the Skills section with usage examples
  and a description of auto-discovery vs explicit loading vs --no-skills

Co-authored-by: Claude <claude@anthropic.com>

* feat: add config file support for skills options

Skills could previously only be controlled via CLI flags or SDK Options
fields. This commit wires all three skills settings into viper so they
can also be set in .kit.yml / .kit.yaml / .kit.json and via KIT_*
environment variables — matching the pattern used by no-extensions,
no-core-tools, and prompt-template.

cmd/root.go:
- Bind --no-skills, --skill, and --skills-dir flags to viper keys
  (no-skills, skill, skills-dir) so config file values flow through.

pkg/kit/kit.go:
- At skill-load time, merge opts fields with viper values:
  - noSkills = opts.NoSkills || v.GetBool("no-skills")
  - skillPaths: opts.Skills if non-empty, else v.GetStringSlice("skill")
  - skillsDir: opts.SkillsDir if non-empty, else v.GetString("skills-dir")
- Build a shallow-copied mergedOpts so loadSkills() picks up the
  resolved values without mutating the original Options struct.

docs:
- README.md: add skills keys to the Basic Configuration YAML example
- www/pages/configuration.md: add no-skills, skill, skills-dir rows to
  the All configuration keys table

Config file example (.kit.yml):
  no-skills: false
  skill:
    - /path/to/skill.md
  skills-dir: /path/to/skills/

Co-authored-by: Claude <claude@anthropic.com>

* config: add skills keys to default .kit.yml template

Add no-skills, skill, and skills-dir as commented-out examples in the
default config file generated by EnsureConfigExists(), alongside the
existing application settings block.

Co-authored-by: Claude <claude@anthropic.com>

* test: add test coverage for skills CLI flags and config keys

Four test locations updated:

pkg/kit/export_test.go:
- Add ConfigStringSliceForTest() helper to expose v.GetStringSlice()
  from the Kit's isolated viper store, needed to assert skill list values.

pkg/kit/kit_test.go (TestNewWithSkillsOptions):
- NoSkills=true: GetSkills() returns empty slice
- SkillsDir=<empty dir>: kit.New() succeeds with zero skills
- Skills=[file]: single explicit skill file is loaded and name parsed correctly

pkg/kit/viper_isolation_test.go:
- TestSkillsViperKeys: no-API-key struct-level checks for NoSkills, Skills,
  and SkillsDir fields on Options
- TestSkillsConfigFileKeys: full kit.New() round-trips via a written .kit.yml
  for each of the three config keys:
    no-skills: true  → GetSkills() returns empty
    skill: [path]    → named skill loaded from config file path
    skills-dir: dir  → custom discovery root accepted without error

internal/config/config_test.go (TestEnsureConfigExists):
- Assert generated ~/.kit.yml template contains '# Skills configuration',
  'no-skills:', and 'skills-dir:' comment blocks.

Co-authored-by: Claude <claude@anthropic.com>

---------

Co-authored-by: Claude <claude@anthropic.com>

README.md

@@ -128,6 +128,12 @@ temperature: 0.7
 stream: true
 thinking-level: off       # off, none, minimal, low, medium, high
 no-core-tools: false      # set to true to disable all built-in core tools
+
+# Skills — all three keys are optional
+no-skills: false          # set to true to disable all skill loading
+skill:                    # explicit skill files/dirs (disables auto-discovery)
+  - /path/to/skill.md
+skills-dir: ""            # override project-local directory for auto-discovery
 ```
 
 All of the above keys can also be set programmatically via the SDK
@@ -203,6 +209,11 @@ mcpServers:
 --prompt-template        Load a specific prompt template by name
 --no-prompt-templates    Disable prompt template loading
 
+# Skills
+--skill                  Load skill file or directory (repeatable)
+--skills-dir             Override the project-local skills directory for auto-discovery
+--no-skills              Disable skill loading (auto-discovery and explicit)
+
 # Generation parameters
 --max-tokens             Maximum tokens in response (default: 8192, auto-raised up to 32768 for models with larger known output limits)
 --temperature            Randomness 0.0-1.0 (default: 0.7)

cmd/root.go

@@ -73,6 +73,11 @@ var (
 	noCoreToolsFlag  bool
 	extensionPaths   []string
 
+	// Skills control
+	noSkillsFlag bool
+	skillsPaths  []string
+	skillsDir    string
+
 	// TLS configuration
 	tlsSkipVerify bool
 
@@ -283,6 +288,14 @@ func init() {
 	rootCmd.PersistentFlags().
 		StringSliceVarP(&extensionPaths, "extension", "e", nil, "load additional extension file(s)")
 
+	// Skills flags
+	rootCmd.PersistentFlags().
+		BoolVar(&noSkillsFlag, "no-skills", false, "disable skill loading (auto-discovery and explicit)")
+	rootCmd.PersistentFlags().
+		StringSliceVar(&skillsPaths, "skill", nil, "load skill file or directory (repeatable)")
+	rootCmd.PersistentFlags().
+		StringVar(&skillsDir, "skills-dir", "", "override the project-local skills directory for auto-discovery")
+
 	flags := rootCmd.PersistentFlags()
 	flags.StringVar(&providerURL, "provider-url", "", "base URL for the provider API (applies to OpenAI, Anthropic, Ollama, and Google)")
 	flags.StringVar(&providerAPIKey, "provider-api-key", "", "API key for the provider (applies to OpenAI, Anthropic, and Google)")
@@ -333,6 +346,9 @@ func init() {
 	_ = viper.BindPFlag("extension", rootCmd.PersistentFlags().Lookup("extension"))
 	_ = viper.BindPFlag("prompt-template", rootCmd.PersistentFlags().Lookup("prompt-template"))
 	_ = viper.BindPFlag("no-prompt-templates", rootCmd.PersistentFlags().Lookup("no-prompt-templates"))
+	_ = viper.BindPFlag("no-skills", rootCmd.PersistentFlags().Lookup("no-skills"))
+	_ = viper.BindPFlag("skill", rootCmd.PersistentFlags().Lookup("skill"))
+	_ = viper.BindPFlag("skills-dir", rootCmd.PersistentFlags().Lookup("skills-dir"))
 
 	// Defaults are already set in flag definitions, no need to duplicate in viper
 
@@ -820,6 +836,9 @@ func runNormalMode(ctx context.Context) error {
 		AutoCompact:      autoCompactFlag,
 		MCPAuthHandler:   authHandler,
 		DisableCoreTools: viper.GetBool("no-core-tools"),
+		NoSkills:         noSkillsFlag,
+		Skills:           skillsPaths,
+		SkillsDir:        skillsDir,
 		// This callback is called when each MCP server finishes loading.
 		// We use a closure that captures appInstancePtr which is set after
 		// app.New() is called below.

internal/config/config.go

@@ -493,6 +493,12 @@ mcpServers:
 #     maxTokens: 16384
 #     systemPrompt: "You are a deep reasoning assistant."  # or a file path
 
+# Skills configuration (all optional)
+# no-skills: false                          # Set to true to disable all skill loading
+# skill:                                    # Explicit skill files/dirs (disables auto-discovery)
+#   - "/path/to/skill.md"
+# skills-dir: "/path/to/skills"            # Override project-local directory for auto-discovery
+
 # API Configuration (can also use environment variables)
 # provider-api-key: "your-api-key"         # API key for OpenAI, Anthropic, or Google
 # provider-url: "https://api.openai.com/v1" # Base URL for OpenAI, Anthropic, or Ollama

internal/config/config_test.go

@@ -205,6 +205,9 @@ func TestEnsureConfigExists(t *testing.T) {
 		"type: \"local\"",
 		"type: \"remote\"",
 		"Core tools",
+		"# Skills configuration",
+		"no-skills:",
+		"skills-dir:",
 	}
 
 	for _, expected := range expectedSections {

pkg/kit/export_test.go

@@ -20,3 +20,9 @@ func (m *Kit) ConfigFloatForTest(key string) float64 { return m.v.GetFloat64(key
 // ConfigBoolForTest returns the bool value of key from this Kit's isolated
 // configuration store.
 func (m *Kit) ConfigBoolForTest(key string) bool { return m.v.GetBool(key) }
+
+// ConfigStringSliceForTest returns the string slice value of key from this
+// Kit's isolated configuration store.
+func (m *Kit) ConfigStringSliceForTest(key string) []string {
+	return m.v.GetStringSlice(key)
+}

pkg/kit/kit.go

@@ -1330,9 +1330,25 @@ func New(ctx context.Context, opts *Options) (*Kit, error) {
 		}
 
 		// Load skills — either from explicit paths or via auto-discovery.
-		if !opts.NoSkills {
+		// Merge viper config with opts: CLI flag / config file values are
+		// already bound to viper by cmd/root.go, so v.GetBool("no-skills"),
+		// v.GetStringSlice("skill"), and v.GetString("skills-dir") capture
+		// both --flag and .kit.yml keys transparently.
+		noSkills := opts.NoSkills || v.GetBool("no-skills")
+		skillPaths := opts.Skills
+		if len(skillPaths) == 0 {
+			skillPaths = v.GetStringSlice("skill")
+		}
+		skillsDir := opts.SkillsDir
+		if skillsDir == "" {
+			skillsDir = v.GetString("skills-dir")
+		}
+		if !noSkills {
+			mergedOpts := *opts
+			mergedOpts.Skills = skillPaths
+			mergedOpts.SkillsDir = skillsDir
 			var err error
-			loadedSkills, err = loadSkills(opts)
+			loadedSkills, err = loadSkills(&mergedOpts)
 			if err != nil {
 				return fmt.Errorf("failed to load skills: %w", err)
 			}

pkg/kit/kit_test.go

@@ -365,6 +365,81 @@ func TestNewSystemPromptFilePath(t *testing.T) {
 	}
 }
 
+// TestNewWithSkillsOptions verifies that the three skills-related Options
+// fields (NoSkills, Skills, SkillsDir) are wired correctly into kit.New().
+func TestNewWithSkillsOptions(t *testing.T) {
+	if os.Getenv("ANTHROPIC_API_KEY") == "" {
+		t.Skip("Skipping test: ANTHROPIC_API_KEY not set")
+	}
+
+	ctx := context.Background()
+
+	t.Run("NoSkills disables skill loading", func(t *testing.T) {
+		host, err := kit.New(ctx, &kit.Options{
+			Model:     "anthropic/claude-sonnet-4-5-20250929",
+			Quiet:     true,
+			NoSession: true,
+			NoSkills:  true,
+		})
+		if err != nil {
+			t.Fatalf("kit.New failed: %v", err)
+		}
+		defer func() { _ = host.Close() }()
+
+		if got := host.GetSkills(); len(got) != 0 {
+			t.Errorf("NoSkills=true: expected 0 skills, got %d", len(got))
+		}
+	})
+
+	t.Run("SkillsDir propagates", func(t *testing.T) {
+		// Use a non-existent dir — no skills will load but the option must be
+		// accepted without error and result in zero skills.
+		dir := t.TempDir()
+		host, err := kit.New(ctx, &kit.Options{
+			Model:     "anthropic/claude-sonnet-4-5-20250929",
+			Quiet:     true,
+			NoSession: true,
+			SkillsDir: dir,
+		})
+		if err != nil {
+			t.Fatalf("kit.New failed: %v", err)
+		}
+		defer func() { _ = host.Close() }()
+
+		// Empty dir → no skills; the important thing is no error.
+		_ = host.GetSkills()
+	})
+
+	t.Run("explicit Skills paths load correctly", func(t *testing.T) {
+		// Write a minimal skill file to a temp dir.
+		dir := t.TempDir()
+		skillFile := dir + "/my-skill.md"
+		content := "---\nname: test-skill\ndescription: A test skill\n---\nDo the thing.\n"
+		if err := os.WriteFile(skillFile, []byte(content), 0o644); err != nil {
+			t.Fatalf("failed to write skill file: %v", err)
+		}
+
+		host, err := kit.New(ctx, &kit.Options{
+			Model:     "anthropic/claude-sonnet-4-5-20250929",
+			Quiet:     true,
+			NoSession: true,
+			Skills:    []string{skillFile},
+		})
+		if err != nil {
+			t.Fatalf("kit.New failed: %v", err)
+		}
+		defer func() { _ = host.Close() }()
+
+		skills := host.GetSkills()
+		if len(skills) != 1 {
+			t.Fatalf("expected 1 skill, got %d", len(skills))
+		}
+		if skills[0].Name != "test-skill" {
+			t.Errorf("skill name = %q; want %q", skills[0].Name, "test-skill")
+		}
+	})
+}
+
 // TestNewSystemPromptInline confirms that inline system-prompt strings still
 // flow through unchanged after the file-path resolution change.
 func TestNewSystemPromptInline(t *testing.T) {

pkg/kit/viper_isolation_test.go

@@ -205,6 +205,131 @@ func TestNewZeroOptionsKeepsStreamingDefault(t *testing.T) {
 	}
 }
 
+// TestSkillsViperKeys verifies that the three skills config keys (no-skills,
+// skill, skills-dir) flow through viper when set via a config file, matching
+// the pattern used by no-extensions and no-core-tools. This test does not
+// require an API key because it only exercises Options struct plumbing.
+func TestSkillsViperKeys(t *testing.T) {
+	t.Run("NoSkills option disables skill loading", func(t *testing.T) {
+		o := &kit.Options{}
+		o.NoSkills = true
+		if !o.NoSkills {
+			t.Error("Options.NoSkills = true not reflected on struct")
+		}
+	})
+
+	t.Run("Skills paths set on Options", func(t *testing.T) {
+		o := &kit.Options{
+			Skills: []string{"/a/skill.md", "/b/skill.md"},
+		}
+		if len(o.Skills) != 2 {
+			t.Errorf("Options.Skills: got %d paths, want 2", len(o.Skills))
+		}
+		if o.Skills[0] != "/a/skill.md" {
+			t.Errorf("Options.Skills[0] = %q; want %q", o.Skills[0], "/a/skill.md")
+		}
+	})
+
+	t.Run("SkillsDir set on Options", func(t *testing.T) {
+		o := &kit.Options{
+			SkillsDir: "/custom/skills",
+		}
+		if o.SkillsDir != "/custom/skills" {
+			t.Errorf("Options.SkillsDir = %q; want %q", o.SkillsDir, "/custom/skills")
+		}
+	})
+}
+
+// TestSkillsConfigFileKeys verifies that no-skills, skill, and skills-dir
+// config file keys are read via viper and applied correctly. Requires an API
+// key because kit.New() is called to exercise the full config-load path.
+func TestSkillsConfigFileKeys(t *testing.T) {
+	if os.Getenv("ANTHROPIC_API_KEY") == "" {
+		t.Skip("Skipping test: ANTHROPIC_API_KEY not set")
+	}
+
+	ctx := context.Background()
+
+	t.Run("no-skills config key disables skill loading", func(t *testing.T) {
+		// Write a config file with no-skills: true.
+		cfgFile := t.TempDir() + "/.kit.yml"
+		if err := os.WriteFile(cfgFile, []byte("no-skills: true\n"), 0o644); err != nil {
+			t.Fatalf("failed to write config: %v", err)
+		}
+
+		host, err := kit.New(ctx, &kit.Options{
+			Model:      "anthropic/claude-sonnet-4-5-20250929",
+			Quiet:      true,
+			NoSession:  true,
+			ConfigFile: cfgFile,
+		})
+		if err != nil {
+			t.Fatalf("kit.New failed: %v", err)
+		}
+		defer func() { _ = host.Close() }()
+
+		if got := host.GetSkills(); len(got) != 0 {
+			t.Errorf("no-skills:true in config: expected 0 skills, got %d", len(got))
+		}
+	})
+
+	t.Run("skill config key loads explicit skill files", func(t *testing.T) {
+		dir := t.TempDir()
+		skillFile := dir + "/cfg-skill.md"
+		if err := os.WriteFile(skillFile, []byte("---\nname: cfg-skill\ndescription: from config\n---\nContent.\n"), 0o644); err != nil {
+			t.Fatalf("failed to write skill file: %v", err)
+		}
+
+		cfgContent := "skill:\n  - " + skillFile + "\n"
+		cfgFile := dir + "/.kit.yml"
+		if err := os.WriteFile(cfgFile, []byte(cfgContent), 0o644); err != nil {
+			t.Fatalf("failed to write config: %v", err)
+		}
+
+		host, err := kit.New(ctx, &kit.Options{
+			Model:      "anthropic/claude-sonnet-4-5-20250929",
+			Quiet:      true,
+			NoSession:  true,
+			ConfigFile: cfgFile,
+		})
+		if err != nil {
+			t.Fatalf("kit.New failed: %v", err)
+		}
+		defer func() { _ = host.Close() }()
+
+		skills := host.GetSkills()
+		if len(skills) != 1 {
+			t.Fatalf("expected 1 skill from config, got %d", len(skills))
+		}
+		if skills[0].Name != "cfg-skill" {
+			t.Errorf("skill name = %q; want %q", skills[0].Name, "cfg-skill")
+		}
+	})
+
+	t.Run("skills-dir config key overrides auto-discovery root", func(t *testing.T) {
+		dir := t.TempDir()
+		cfgContent := "skills-dir: " + dir + "\n"
+		cfgFile := dir + "/.kit.yml"
+		if err := os.WriteFile(cfgFile, []byte(cfgContent), 0o644); err != nil {
+			t.Fatalf("failed to write config: %v", err)
+		}
+
+		host, err := kit.New(ctx, &kit.Options{
+			Model:      "anthropic/claude-sonnet-4-5-20250929",
+			Quiet:      true,
+			NoSession:  true,
+			ConfigFile: cfgFile,
+		})
+		if err != nil {
+			t.Fatalf("kit.New failed: %v", err)
+		}
+		defer func() { _ = host.Close() }()
+
+		// Empty dir → 0 skills; the key point is no error during init.
+		_ = host.GetSkills()
+	})
+}
+
 // TestNewStreamingExplicitOptOut verifies that a raw Options can still disable
 // streaming by setting Streaming to a pointer to false.
 func TestNewStreamingExplicitOptOut(t *testing.T) {

www/pages/cli/commands.md

@@ -56,6 +56,26 @@ kit install --all            # Install all extensions without prompting
 kit skill                    # Install the Kit extensions skill via skills.sh
 ```
 
+### Skills CLI flags
+
+Control which skills are loaded at startup:
+
+```bash
+# Load a specific skill file
+kit --skill path/to/skill.md "prompt"
+
+# Load multiple skill files or directories (flag is repeatable)
+kit --skill ./skill1.md --skill ./skill2.md "prompt"
+
+# Load all skills from a custom directory instead of the default locations
+kit --skills-dir /path/to/skills "prompt"
+
+# Disable all skill loading (auto-discovery and explicit)
+kit --no-skills "prompt"
+```
+
+Skills are auto-discovered from `~/.config/kit/skills/`, `.kit/skills/`, and `.agents/skills/` by default. Use `--skills-dir` to override the project-local search root, or `--skill` to load files explicitly (which disables auto-discovery). `--no-skills` suppresses all skill loading regardless of other flags.
+
 ## Interactive slash commands
 
 These commands are available inside the Kit TUI during an interactive session:

www/pages/cli/flags.md

@@ -48,6 +48,14 @@ These flags control Kit's behavior. When a prompt is passed as a positional argu
 | `--prompt-template` | — | — | Load a specific prompt template by name |
 | `--no-prompt-templates` | — | `false` | Disable prompt template loading |
 
+## Skills
+
+| Flag | Short | Default | Description |
+|------|-------|---------|-------------|
+| `--skill` | — | — | Load skill file or directory (repeatable) |
+| `--skills-dir` | — | — | Override the project-local skills directory for auto-discovery |
+| `--no-skills` | — | `false` | Disable skill loading (auto-discovery and explicit) |
+
 ## Generation parameters
 
 | Flag | Short | Default | Description |

www/pages/configuration.md

@@ -47,6 +47,9 @@ stream: true
 | `theme` | object or string | — | UI theme ([inline overrides or file path](/themes)) |
 | `prompt-templates` | bool | `true` | Enable prompt template loading |
 | `prompt-template` | string | — | Specific template to load by name |
+| `no-skills` | bool | `false` | Disable skill loading (auto-discovery and explicit) |
+| `skill` | list | — | Explicit skill files or directories to load (disables auto-discovery) |
+| `skills-dir` | string | — | Override the project-local directory used for skill auto-discovery |
 
 ## Environment variables