fix(kit): resolve system-prompt file path before PromptBuilder (#25)

When system-prompt was a file path (via --system-prompt, config entry,
or SDK Options.SystemPrompt), the path string itself was used as the
base prompt because config.LoadSystemPrompt only ran later in
BuildProviderConfig — by which point viper had been overwritten with
the path-augmented composed text. The LLM received the path instead of
the prompt contents.

- Call config.LoadSystemPrompt on the raw viper value in New() before
  PromptBuilder composes runtime context (AGENTS.md / skills / date).
- Add HasCustomSystemPrompt() and GetSystemPromptSource() so SDK callers
  can inspect prompt state without reaching into viper.
- Display 'System Prompt loaded: <source>' at startup in CLI and TUI
  modes, paralleling the per-server 'MCP server loaded' notice.
- Add regression tests covering both file-path and inline prompt paths.

Fixes #25

cmd/root.go

@@ -784,6 +784,16 @@ func runNormalMode(ctx context.Context) error {
 	}
 	defer func() { _ = kitInstance.Close() }()
 
+	// Build the "System Prompt loaded" notice shown at startup, paralleling the
+	// per-server "MCP server loaded" notifications so users can confirm that a
+	// configured prompt file was found and applied.
+	var systemPromptLoadedMsg string
+	if kitInstance.HasCustomSystemPrompt() {
+		if src := kitInstance.GetSystemPromptSource(); src != "" {
+			systemPromptLoadedMsg = "System Prompt loaded: " + src
+		}
+	}
+
 	// Extract metadata for display and app options.
 	parsedProvider, modelName, serverNames, toolNames, mcpToolCount, extensionToolCount := CollectAgentMetadata(kitInstance, mcpConfig)
 
@@ -801,6 +811,9 @@ func runNormalMode(ctx context.Context) error {
 		}
 
 		DisplayDebugConfig(cli, kitInstance, mcpConfig, parsedProvider)
+		if systemPromptLoadedMsg != "" {
+			cli.DisplayInfo(systemPromptLoadedMsg)
+		}
 	}
 
 	// Load existing messages from resumed/continued sessions.
@@ -840,6 +853,9 @@ func runNormalMode(ctx context.Context) error {
 
 	// Buffer for extension messages during startup (printed after startup banner).
 	var startupExtensionMessages []string
+	if systemPromptLoadedMsg != "" {
+		startupExtensionMessages = append(startupExtensionMessages, systemPromptLoadedMsg)
+	}
 
 	// Set up extension context and emit SessionStart.
 	if kitInstance.Extensions().HasExtensions() {

pkg/kit/kit.go

@@ -58,6 +58,9 @@ type Kit struct {
 	// When false, per-model system prompts from modelSettings/customModels
 	// can replace the default prompt on model switch.
 	hasCustomSystemPrompt bool
+	// systemPromptSource holds the raw configured value (file path or text)
+	// when hasCustomSystemPrompt is true; empty when the built-in default is in use.
+	systemPromptSource string
 
 	// Hook registries — interception layer (see hooks.go).
 	beforeToolCall  *hookRegistry[BeforeToolCallHook, BeforeToolCallResult]
@@ -632,6 +635,21 @@ func (m *Kit) SetModel(ctx context.Context, modelString string) error {
 	return nil
 }
 
+// HasCustomSystemPrompt reports whether the user explicitly configured a system
+// prompt via --system-prompt, a config file entry, or SDK Options.SystemPrompt.
+// When false, the built-in default (or a per-model override) is in use and can
+// be replaced transparently on model switch.
+func (m *Kit) HasCustomSystemPrompt() bool {
+	return m.hasCustomSystemPrompt
+}
+
+// GetSystemPromptSource returns the raw configured value — a file path or
+// inline text — when HasCustomSystemPrompt is true; returns an empty string
+// when the built-in default prompt is active.
+func (m *Kit) GetSystemPromptSource() string {
+	return m.systemPromptSource
+}
+
 // composeSystemPrompt takes a base system prompt and composes it with the
 // current runtime context: AGENTS.md content, skills metadata, and date/cwd.
 // This mirrors the composition done during Kit.New() initialization.
@@ -1179,6 +1197,7 @@ func New(ctx context.Context, opts *Options) (*Kit, error) {
 		maxSteps              int
 		streaming             bool
 		hasCustomSystemPrompt bool
+		systemPromptSource    string
 	)
 
 	if err := func() error {
@@ -1285,13 +1304,27 @@ func New(ctx context.Context, opts *Options) (*Kit, error) {
 		// explicitly set system-prompt, use the per-model prompt as the
 		// base instead of the global default.
 		{
-			basePrompt := viper.GetString("system-prompt")
+			rawPromptInput := viper.GetString("system-prompt")
+
+			// Resolve a file path to its content so PromptBuilder receives the
+			// actual prompt text rather than a literal path string. Without this,
+			// when system-prompt is set to a file path in the config file or via
+			// --system-prompt, the path itself becomes the effective system prompt
+			// sent to the model (LoadSystemPrompt only ran later, after viper had
+			// been overwritten with the augmented base text).
+			basePrompt, _ := config.LoadSystemPrompt(rawPromptInput)
+			if basePrompt == "" {
+				basePrompt = rawPromptInput
+			}
 
 			// Track whether the user explicitly configured a custom system
 			// prompt. When they haven't (basePrompt is the built-in default
 			// or empty), per-model system prompts can replace it on switch.
 			userSetSystemPrompt := basePrompt != "" && basePrompt != defaultSystemPrompt
 			hasCustomSystemPrompt = userSetSystemPrompt
+			if hasCustomSystemPrompt {
+				systemPromptSource = rawPromptInput
+			}
 
 			// Check for per-model system prompt override when no explicit
 			// global system-prompt was configured by the user.
@@ -1500,6 +1533,7 @@ func New(ctx context.Context, opts *Options) (*Kit, error) {
 		opts:                  opts,
 		mcpConfig:             mcpConfig,
 		hasCustomSystemPrompt: hasCustomSystemPrompt,
+		systemPromptSource:    systemPromptSource,
 		beforeToolCall:        beforeToolCall,
 		afterToolResult:       afterToolResult,
 		beforeTurn:            beforeTurn,

pkg/kit/kit_test.go

@@ -3,6 +3,7 @@ package kit_test
 import (
 	"context"
 	"os"
+	"strings"
 	"testing"
 
 	"github.com/spf13/viper"
@@ -306,3 +307,92 @@ func TestSessionManagement(t *testing.T) {
 // resetViper wipes viper's global state so a test case doesn't leak
 // viper.Set() calls into the next one. Used via defer in subtests.
 func resetViper() { viper.Reset() }
+
+// TestNewSystemPromptFilePath is a regression test for issue #25.
+//
+// When Options.SystemPrompt (or the --system-prompt flag / config entry) is a
+// file path, Kit must resolve the path to its file contents *before* the
+// PromptBuilder composes the runtime context. Previously the path string
+// itself was used verbatim as the base prompt, so the LLM received the path —
+// not the prompt — as its system message.
+func TestNewSystemPromptFilePath(t *testing.T) {
+	if os.Getenv("ANTHROPIC_API_KEY") == "" {
+		t.Skip("Skipping test: ANTHROPIC_API_KEY not set")
+	}
+	defer resetViper()
+
+	const promptContent = "You are a strict regression-test persona. Marker: KIT-25-OK"
+
+	tmpFile, err := os.CreateTemp(t.TempDir(), "kit-system-prompt-*.md")
+	if err != nil {
+		t.Fatalf("failed to create temp prompt file: %v", err)
+	}
+	if _, err := tmpFile.WriteString(promptContent); err != nil {
+		t.Fatalf("failed to write temp prompt file: %v", err)
+	}
+	if err := tmpFile.Close(); err != nil {
+		t.Fatalf("failed to close temp prompt file: %v", err)
+	}
+
+	ctx := context.Background()
+	host, err := kit.New(ctx, &kit.Options{
+		Model:        "anthropic/claude-sonnet-4-5-20250929",
+		SystemPrompt: tmpFile.Name(),
+		Quiet:        true,
+		NoSession:    true,
+	})
+	if err != nil {
+		t.Fatalf("Failed to create Kit with system-prompt file: %v", err)
+	}
+	defer func() { _ = host.Close() }()
+
+	if !host.HasCustomSystemPrompt() {
+		t.Error("HasCustomSystemPrompt() = false; want true when --system-prompt is set")
+	}
+	if got, want := host.GetSystemPromptSource(), tmpFile.Name(); got != want {
+		t.Errorf("GetSystemPromptSource() = %q; want %q", got, want)
+	}
+
+	// The composed system prompt is written back to viper after PromptBuilder
+	// runs. It must contain the file's contents, not the file path.
+	composed := viper.GetString("system-prompt")
+	if !strings.Contains(composed, promptContent) {
+		t.Errorf("composed system-prompt does not contain file contents\n  composed = %q\n  want substring = %q", composed, promptContent)
+	}
+	if strings.TrimSpace(composed) == tmpFile.Name() {
+		t.Errorf("composed system-prompt is the file path verbatim (%q); LoadSystemPrompt was not applied before PromptBuilder", composed)
+	}
+}
+
+// TestNewSystemPromptInline confirms that inline system-prompt strings still
+// flow through unchanged after the file-path resolution change.
+func TestNewSystemPromptInline(t *testing.T) {
+	if os.Getenv("ANTHROPIC_API_KEY") == "" {
+		t.Skip("Skipping test: ANTHROPIC_API_KEY not set")
+	}
+	defer resetViper()
+
+	const inline = "You are a concise inline-prompt persona."
+
+	ctx := context.Background()
+	host, err := kit.New(ctx, &kit.Options{
+		Model:        "anthropic/claude-sonnet-4-5-20250929",
+		SystemPrompt: inline,
+		Quiet:        true,
+		NoSession:    true,
+	})
+	if err != nil {
+		t.Fatalf("Failed to create Kit with inline system-prompt: %v", err)
+	}
+	defer func() { _ = host.Close() }()
+
+	if !host.HasCustomSystemPrompt() {
+		t.Error("HasCustomSystemPrompt() = false; want true for inline prompt")
+	}
+	if got := host.GetSystemPromptSource(); got != inline {
+		t.Errorf("GetSystemPromptSource() = %q; want %q", got, inline)
+	}
+	if composed := viper.GetString("system-prompt"); !strings.Contains(composed, inline) {
+		t.Errorf("composed system-prompt missing inline content; got %q", composed)
+	}
+}