feat(tools): repo_tree, repo_topics_update, file_read dir fix (#14, #15, #18)

repo_tree: GET /git/trees/{ref}?recursive=1 — full recursive file tree
repo_topics_update: PUT /repos/{owner}/{repo}/topics — replace topic list
file_read: detect array response and return descriptive error for dir paths

internal/tools/file_read_test.go

@@ -57,6 +57,21 @@ func TestFileReadToolDefaultBranchResolution(t *testing.T) {
 	assert.Equal(t, "main", result["ref"])
 }
 
+func TestFileReadOnDirReturnsDescriptiveError(t *testing.T) {
+	srv := httptest.NewServer(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
+		// Gitea returns an array when path is a directory
+		w.Header().Set("Content-Type", "application/json")
+		_, _ = w.Write([]byte(`[{"name":"README.md","path":"internal/README.md","type":"file","sha":"abc"}]`))
+	}))
+	defer srv.Close()
+
+	tool := tools.NewFileRead(gitea.NewClient(srv.URL, "tok"), allowlist.New([]string{"mathias"}))
+	_, err := tool.Call(context.Background(), json.RawMessage(`{"owner":"mathias","name":"infra","path":"internal","ref":"main"}`))
+	require.Error(t, err)
+	assert.Contains(t, err.Error(), "directory")
+	assert.Contains(t, err.Error(), "dir_list")
+}
+
 func TestFileReadAllowlistRejects(t *testing.T) {
 	tool := tools.NewFileRead(gitea.NewClient("http://unused", ""), allowlist.New([]string{"mathias"}))
 	_, err := tool.Call(context.Background(), json.RawMessage(`{"owner":"evil","name":"infra","path":"README.md"}`))