fix(mcp): read .claude.json + mcp_servers.json, handle type/transport + array commands

internal/adapters/claudecode/claudecode.go

@@ -78,21 +78,41 @@ func (a *Adapter) Render(b *canonical.Bundle) (*adapter.FileSet, error) {
 		Content: []byte(instructions),
 	})
 
-	settingsPath := filepath.Join(base, "settings.json")
-	existing, _ := os.ReadFile(settingsPath)
-	overlay := map[string]any{
-		"mcpServers": common.BuildMCPMapStyled(&b.MCP, common.MCPClaudeStyle),
-	}
-	merged, err := common.MergeJSONKeys(existing, overlay)
+	// Claude Code reads MCP servers from two files on disk:
+	//   * ~/.claude.json (live, written by `claude mcp add`)
+	//   * ~/.claude/mcp_servers.json (older / fallback location)
+	// Write the dedicated file as the canonical destination, AND merge the
+	// same map into ~/.claude.json (preserving every other key in that
+	// large state file) so both stay in sync.
+	mcpMap := common.BuildMCPMapStyled(&b.MCP, common.MCPClaudeStyle)
+	overlay := map[string]any{"mcpServers": mcpMap}
+
+	dedicatedPath := filepath.Join(base, "mcp_servers.json")
+	dedicatedExisting, _ := os.ReadFile(dedicatedPath)
+	dedicatedMerged, err := common.MergeJSONKeys(dedicatedExisting, overlay)
 	if err != nil {
 		return nil, err
 	}
 	fs.Add(adapter.File{
-		Dest:    settingsPath,
+		Dest:    dedicatedPath,
 		Kind:    adapter.RenderedFile,
-		Content: merged,
+		Content: dedicatedMerged,
 	})
 
+	livePath := filepath.Join(a.home, ".claude.json")
+	if _, err := os.Stat(livePath); err == nil {
+		liveExisting, _ := os.ReadFile(livePath)
+		liveMerged, err := common.MergeJSONKeys(liveExisting, overlay)
+		if err != nil {
+			return nil, err
+		}
+		fs.Add(adapter.File{
+			Dest:    livePath,
+			Kind:    adapter.RenderedFile,
+			Content: liveMerged,
+		})
+	}
+
 	return fs, nil
 }
 

internal/adapters/claudecode/claudecode_test.go

@@ -42,25 +42,28 @@ func TestRenderProducesExpectedTargets(t *testing.T) {
 	assert.Equal(t, adapter.RenderedFile, seen[claudemdDest].Kind)
 	assert.Contains(t, string(seen[claudemdDest].Content), "# global")
 
-	settingsDest := filepath.Join(home, ".claude", "settings.json")
-	assert.Equal(t, adapter.RenderedFile, seen[settingsDest].Kind)
-	settingsBody := string(seen[settingsDest].Content)
-	assert.Contains(t, settingsBody, "filepuff")
-	assert.Contains(t, settingsBody, "/bin/filepuff")
+	mcpDest := filepath.Join(home, ".claude", "mcp_servers.json")
+	assert.Equal(t, adapter.RenderedFile, seen[mcpDest].Kind)
+	body := string(seen[mcpDest].Content)
+	assert.Contains(t, body, "filepuff")
+	assert.Contains(t, body, "/bin/filepuff")
+	assert.Contains(t, body, "\"type\": \"stdio\"")
 }
-func TestRenderMergesExistingSettings(t *testing.T) {
+func TestRenderMergesLiveClaudeJSON(t *testing.T) {
 	home := t.TempDir()
 	base := filepath.Join(home, ".claude")
 	require.NoError(t, os.MkdirAll(base, 0o750))
 
-	// Existing settings.json with user-managed keys.
+	// Existing ~/.claude.json with user-managed top-level keys.
 	existing := map[string]any{
-		"hooks":       map[string]any{"preToolUse": []string{"/bin/hook"}},
-		"permissions": map[string]any{"allow": []string{"Bash"}},
-		"env":         map[string]any{"ANTHROPIC_DEFAULT_MODEL": "opus"},
+		"projects":         map[string]any{"/path": map[string]any{"x": 1}},
+		"shellIntegration": true,
+		"mcpServers": map[string]any{
+			"old": map[string]any{"command": "/bin/old", "type": "stdio"},
+		},
 	}
 	body, _ := json.Marshal(existing)
-	require.NoError(t, os.WriteFile(filepath.Join(base, "settings.json"), body, 0o600))
+	require.NoError(t, os.WriteFile(filepath.Join(home, ".claude.json"), body, 0o600))
 
 	ad := New(WithHome(home))
 	b := &canonical.Bundle{
@@ -75,20 +78,20 @@ func TestRenderMergesExistingSettings(t *testing.T) {
 	seen := map[string]adapter.File{}
 	fs.ForEach(func(f adapter.File) { seen[f.Dest] = f })
 
-	settingsDest := filepath.Join(base, "settings.json")
+	livePath := filepath.Join(home, ".claude.json")
 	var parsed map[string]any
-	require.NoError(t, json.Unmarshal(seen[settingsDest].Content, &parsed))
+	require.NoError(t, json.Unmarshal(seen[livePath].Content, &parsed))
 
-	// User keys preserved.
-	assert.Contains(t, parsed, "hooks")
-	assert.Contains(t, parsed, "permissions")
-	assert.Contains(t, parsed, "env")
-	// MCP updated.
+	// User-managed top-level keys preserved.
+	assert.Contains(t, parsed, "projects")
+	assert.Contains(t, parsed, "shellIntegration")
+	// mcpServers replaced with canonical content.
 	mcp := parsed["mcpServers"].(map[string]any)
 	assert.Contains(t, mcp, "filepuff")
-	// MCP entries must NOT have a "type" field (claude-code style).
+	assert.NotContains(t, mcp, "old")
+	// Each entry uses Claude's "type" key.
 	fp := mcp["filepuff"].(map[string]any)
-	assert.NotContains(t, fp, "type")
+	assert.Equal(t, "stdio", fp["type"])
 }
 
 func TestImport(t *testing.T) {
@@ -107,16 +110,17 @@ func TestImport(t *testing.T) {
 		filepath.Join(base, "CLAUDE.md"),
 		[]byte("# global"), 0o600))
 
-	settings, _ := json.Marshal(map[string]any{
+	// Live ~/.claude.json with mcpServers (the primary location).
+	liveBody, _ := json.Marshal(map[string]any{
 		"mcpServers": map[string]any{
 			"filepuff": map[string]any{
-				"command":   "/bin/filepuff",
-				"transport": "stdio",
+				"command": "/bin/filepuff",
+				"type":    "stdio",
 			},
 		},
 	})
 	require.NoError(t, os.WriteFile(
-		filepath.Join(base, "settings.json"), settings, 0o600))
+		filepath.Join(home, ".claude.json"), liveBody, 0o600))
 
 	ad := New(WithHome(home))
 	res, err := ad.Import(home)

internal/adapters/claudecode/import.go

@@ -38,10 +38,27 @@ func importFrom(home string) (*adapter.ImportResult, error) {
 	}
 	res.Instructions = body
 
-	servers, err := common.ImportMCPFromJSONFile(filepath.Join(base, "settings.json"), "mcpServers")
-	if err != nil {
-		return nil, err
+	// Claude Code stores MCP servers across several files. Read all known
+	// locations and dedupe by name; ~/.claude.json is the live source so
+	// its entries win on conflict.
+	mcpSources := []string{
+		filepath.Join(home, ".claude.json"),
+		filepath.Join(base, "mcp_servers.json"),
+		filepath.Join(base, "settings.json"),
+	}
+	seen := map[string]bool{}
+	for _, p := range mcpSources {
+		servers, err := common.ImportMCPFromJSONFile(p, "mcpServers")
+		if err != nil {
+			return nil, err
+		}
+		for _, s := range servers {
+			if seen[s.Name] {
+				continue
+			}
+			seen[s.Name] = true
+			res.MCP = append(res.MCP, s)
+		}
 	}
-	res.MCP = servers
 	return res, nil
 }