fix: handle empty files in get_file_contents (#2042)

1. Empty (0-byte) files caused an unhandled error because the GitHub API
   returns null content with base64 encoding for them; GetContent() fails
   with "malformed response: base64 encoding of null content". Return
   empty text/plain content directly, bypassing decoding entirely.

Co-authored-by: Ksenia Bobrova <almaleksia@github.com>

Author: kubajanusz

pkg/github/repositories.go

@@ -726,6 +726,20 @@ func GetFileContents(t translations.TranslationHelperFunc) inventory.ServerTool
 					successNote = fmt.Sprintf(" Note: the provided ref '%s' does not exist, default branch '%s' was used instead.", originalRef, rawOpts.Ref)
 				}
 
+				// Empty files (0 bytes) have no content to decode; return
+				// them directly as empty text to avoid errors from
+				// GetContent when the API returns null content with a
+				// base64 encoding field, and to avoid DetectContentType
+				// misclassifying them as binary.
+				if fileSize == 0 {
+					result := &mcp.ResourceContents{
+						URI:      resourceURI,
+						Text:     "",
+						MIMEType: "text/plain",
+					}
+					return utils.NewToolResultResource(fmt.Sprintf("successfully downloaded empty file (SHA: %s)%s", fileSHA, successNote), result), nil, nil
+				}
+
 				// For files >= 1MB, return a ResourceLink instead of content
 				const maxContentSize = 1024 * 1024 // 1MB
 				if fileSize >= maxContentSize {

pkg/github/repositories_test.go

@@ -351,6 +351,40 @@ func Test_GetFileContents(t *testing.T) {
 				Title: "File: large-file.bin",
 			},
 		},
+		{
+			name: "successful empty file content fetch",
+			mockedClient: MockHTTPClientWithHandlers(map[string]http.HandlerFunc{
+				GetReposGitRefByOwnerByRepoByRef: mockResponse(t, http.StatusOK, "{\"ref\": \"refs/heads/main\", \"object\": {\"sha\": \"\"}}"),
+				GetReposByOwnerByRepo:            mockResponse(t, http.StatusOK, "{\"name\": \"repo\", \"default_branch\": \"main\"}"),
+				GetReposContentsByOwnerByRepoByPath: func(w http.ResponseWriter, _ *http.Request) {
+					w.WriteHeader(http.StatusOK)
+					fileContent := &github.RepositoryContent{
+						Name:     github.Ptr(".gitkeep"),
+						Path:     github.Ptr(".gitkeep"),
+						SHA:      github.Ptr("empty123"),
+						Type:     github.Ptr("file"),
+						Content:  nil,
+						Size:     github.Ptr(0),
+						Encoding: github.Ptr("base64"),
+					}
+					contentBytes, _ := json.Marshal(fileContent)
+					_, _ = w.Write(contentBytes)
+				},
+			}),
+			requestArgs: map[string]any{
+				"owner": "owner",
+				"repo":  "repo",
+				"path":  ".gitkeep",
+				"ref":   "refs/heads/main",
+			},
+			expectError: false,
+			expectedResult: mcp.ResourceContents{
+				URI:      "repo://owner/repo/refs/heads/main/contents/.gitkeep",
+				Text:     "",
+				MIMEType: "text/plain",
+			},
+			expectedMsg: "successfully downloaded empty file",
+		},
 		{
 			name: "content fetch fails",
 			mockedClient: MockHTTPClientWithHandlers(map[string]http.HandlerFunc{