Use a transformer to initialize custom elements and call initMethod. This is the

pkg/polymer/lib/src/build/script_compactor.dart

Index: pkg/polymer/lib/src/build/script_compactor.dart
diff --git a/pkg/polymer/lib/src/build/script_compactor.dart b/pkg/polymer/lib/src/build/script_compactor.dart
index e869a2cb55c253bf7ffcc6f26bde5078241dcec8..4392f4d070a7d6cd581a6d9e0fee623ec811b557 100644
--- a/pkg/polymer/lib/src/build/script_compactor.dart
+++ b/pkg/polymer/lib/src/build/script_compactor.dart
@@ -8,9 +8,15 @@ library polymer.src.build.script_compactor;
 import 'dart:async';
 import 'dart:convert';
 
+import 'package:analyzer/src/generated/ast.dart';
+import 'package:analyzer/src/generated/error.dart';
+import 'package:analyzer/src/generated/java_core.dart' show CharSequence;
+import 'package:analyzer/src/generated/parser.dart';
+import 'package:analyzer/src/generated/scanner.dart';
 import 'package:barback/barback.dart';
 import 'package:html5lib/parser.dart' show parseFragment;
 import 'package:path/path.dart' as path;
+import 'package:source_maps/span.dart' show SourceFile;
 
 import 'code_extractor.dart'; // import just for documentation.
 import 'common.dart';
@@ -77,6 +83,7 @@ class ScriptCompactor extends Transformer with PolymerTransformer {
           return null;
         }
 
+        // Emit the bootstrap .dart file
         var bootstrapId = id.addExtension('_bootstrap.dart');
         mainScriptTag.attributes['src'] =
             path.url.basename(bootstrapId.path);
@@ -92,20 +99,159 @@ class ScriptCompactor extends Transformer with PolymerTransformer {
 
         buffer..write('\n')
             ..writeln('void main() {')
-            ..writeln('  configureForDeployment([')
-            ..writeAll(urls.map((url) => "      '$url',\n"))
-            ..writeln('    ]);')
-            ..writeln('  i${i - 1}.main();')
-            ..writeln('}');
-
-        transform.addOutput(new Asset.fromString(
-              bootstrapId, buffer.toString()));
-        transform.addOutput(new Asset.fromString(id, document.outerHtml));
+            ..writeln('  configureForDeployment([');
+
+        // Inject @CustomTag and @initMethod initializations for each library
+        // that is sourced in a script tag.
+        i = 0;
+        return Future.forEach(libraries, (lib) {
+          return _initializersOf(lib, transform, logger).then((initializers) {
+            for (var init in initializers) {
+              var code = init.asCode('i$i');
+              buffer.write("      $code,\n");
+            }
+            i++;
+          });
+        }).then((_) {
+          buffer..writeln('    ]);')
+              ..writeln('  i${urls.length - 1}.main();')
+              ..writeln('}');
+
+          transform.addOutput(new Asset.fromString(
+                bootstrapId, buffer.toString()));
+          transform.addOutput(new Asset.fromString(id, document.outerHtml));
+        });
+      });
+    });
+  }
+
+  /**
+   * Computes the initializers of [dartLibrary]. That is, a closure that calls
+   * Polymer.register for each @CustomTag, and any public top-level methods
+   * labeled with @initMethod.
+   */
+  Future<List<_Initializer>> _initializersOf(
+      AssetId dartLibrary, Transform transform, TransformLogger logger) {
+    var initializers = [];
+    return transform.readInputAsString(dartLibrary).then((code) {
+      var url = dartLibrary.path.startsWith('lib/')

[Jennifer Messerly, 2014/02/03 19:09:32]

refactor this into a function?

[Siggi Cherem (dart-lang), 2014/02/04 00:20:35]

Done.

+            ? 'package:${dartLibrary.package}/${dartLibrary.path.substring(4)}'
+            : dartLibrary.path;
+      var file = new SourceFile.text(url, code);
+      var unit = _parseCompilationUnit(code);
+
+      return Future.forEach(unit.directives, (directive) {
+        // Include anything from parts.
+        if (directive is PartDirective) {
+          var targetId = resolve(dartLibrary, directive.uri.stringValue,
+              logger, _getSpan(file, directive), allowPackageColonUrls: true);
+          return _initializersOf(targetId, transform, logger)
+              .then(initializers.addAll);
+        }
+
+        // Similarly, include anything from exports except what's filtered by
+        // the show/hide combinators.

[Jennifer Messerly, 2014/02/03 19:09:32]

hmm. This seems to be reimplementing top level name resolution?

Not saying this is wrong, but would be good to reuse an impl from dart2js or
dartanalyzer ... touching the show/hide stuff makes me a little nervous because
it seems like the kind of thing that could change and might have resolution
subtleties. 

[Siggi Cherem (dart-lang), 2014/02/04 00:20:35]

I hear you - I've added a TODO. I'm afraid of using that part of the analyzer
because it requires bringing in the full resolution.

+        if (directive is ExportDirective) {
+          var targetId = resolve(dartLibrary, directive.uri.stringValue,

[Jennifer Messerly, 2014/02/03 19:09:32]

idea: pull this out into a separate method? e.g. _processExportDirective.
similar below for ClassDecl and FunctionDecl

[Siggi Cherem (dart-lang), 2014/02/04 00:20:35]

Funny, I thought of it too, but wasn't sure it was worth it. It definitely makes
the code cleaner. Done.

+              logger, _getSpan(file, directive), allowPackageColonUrls: true);
+          return _initializersOf(targetId, transform, logger).then((result) {
+            for (var combinator in directive.combinators) {
+              if (combinator is ShowCombinator) {
+                var show = combinator.shownNames.map((n) => n.name).toSet();
+                result.retainWhere((e) => show.contains(e.symbolName));
+              } else if (combinator is HideCombinator) {
+                var hide = combinator.hiddenNames.map((n) => n.name).toSet();
+                result.removeWhere((e) => hide.contains(e.symbolName));
+              }
+            }
+            initializers.addAll(result);
+          });
+        }
+      }).then((_) {
+        // Scan the code for classes and top-level functions.
+        for (var node in unit.declarations) {

[Jennifer Messerly, 2014/02/03 19:09:32]

is it possible for the library to conflict with an export or part? I think not
because would be an error in Dart too, so should be okay. Just checking.

[Siggi Cherem (dart-lang), 2014/02/04 00:20:35]

yeah, I think that would be caught as a Dart error too.

+          if (node is ClassDeclaration) {
+            for (var meta in node.metadata) {
+              if (!_isCustomTagAnnotation(meta)) continue;
+              var args = meta.arguments.arguments;
+              if (args == null || args.length == 0) {
+                logger.error('Missing argument in @CustomTag annotation',
+                    span: _getSpan(file, meta));
+                continue;
+              }
+
+              var tagName = args[0].stringValue;
+              var typeName = node.name.name;
+              if (typeName.startsWith('_')) {
+                logger.error('@CustomTag is no longer supported on private '
+                  'classes: $tagName', span: _getSpan(file, node.name));
+                continue;
+              }
+              initializers.add(new _CustomTagInitializer(tagName, typeName));
+            }
+          } else if (node is FunctionDeclaration &&
+              node.metadata.any(_isInitMethodAnnotation)) {
+            var methodName = node.name.name;
+            if (methodName.startsWith('_')) {
+              logger.error('@initMethod is no longer supported on private '
+                'functions: $methodName', span: _getSpan(file, node.name));
+              continue;
+            }
+            initializers.add(new _InitMethodInitializer(methodName));
+          }
+        }
+        return initializers;
       });
     });
   }
 }
 
+/** Parse [code] using analyzer. */
+CompilationUnit _parseCompilationUnit(String code) {
+  var errorListener = new _ErrorCollector();
+  var reader = new CharSequenceReader(new CharSequence(code));
+  var scanner = new Scanner(null, reader, errorListener);
+  var token = scanner.tokenize();
+  var parser = new Parser(null, errorListener);
+  return parser.parseCompilationUnit(token);
+}
+
+class _ErrorCollector extends AnalysisErrorListener {
+  final errors = <AnalysisError>[];
+  onError(error) => errors.add(error);
+}
+
+// TODO(sigmund): consider support for importing annotations with prefixes.
+bool _isInitMethodAnnotation(Annotation node) =>
+    node.name.name == 'initMethod' && node.constructorName == null &&
+    node.arguments == null;
+bool _isCustomTagAnnotation(Annotation node) => node.name.name == 'CustomTag';
+
+abstract class _Initializer {
+  String get symbolName;
+  String asCode(String prefix);
+}
+
+class _InitMethodInitializer implements _Initializer {
+  String methodName;
+  String get symbolName => methodName;
+  _InitMethodInitializer(this.methodName);
+
+  String asCode(String prefix) => "$prefix.$methodName";
+}
+
+class _CustomTagInitializer implements _Initializer {
+  String tagName;
+  String typeName;
+  String get symbolName => typeName;
+  _CustomTagInitializer(this.tagName, this.typeName);
+
+  String asCode(String prefix) =>
+      "() => Polymer.register('$tagName', $prefix.$typeName)";
+}
+
+_getSpan(SourceFile file, ASTNode node) => file.span(node.offset, node.end);
+
 const MAIN_HEADER = """
 library app_bootstrap;