diff --git a/.cirrus.yml b/.cirrus.yml
index edefc19..54c4c37 100644
--- a/.cirrus.yml
+++ b/.cirrus.yml
@@ -72,7 +72,7 @@
         - cd script/tool
         - dart analyze --fatal-infos
       script:
-        - ./script/tool_runner.sh analyze
+        - ./script/tool_runner.sh analyze --custom-analysis=script/configs/custom_analysis.yaml
     ### Android tasks ###
     - name: build_all_plugins_apk
       env:
@@ -137,22 +137,6 @@
           CHANNEL: "stable"
         MAPS_API_KEY: ENCRYPTED[596a9f6bca436694625ac50851dc5da6b4d34cba8025f7db5bc9465142e8cd44e15f69e3507787753accebfc4910d550]
         GCLOUD_FIREBASE_TESTLAB_KEY: ENCRYPTED[07586610af1fdfc894e5969f70ef2458341b9b7e9c3b7c4225a663b4a48732b7208a4d91c3b7d45305a6b55fa2a37fc4]
-        # Currently missing harness files (https://github.com/flutter/flutter/issues/86749):
-        #   camera/camera
-        #   google_sign_in/google_sign_in
-        #   in_app_purchase/in_app_purchase
-        #   in_app_purchase_android
-        #   quick_actions
-        #   shared_preferences/shared_preferences
-        #   url_launcher/url_launcher
-        #   video_player/video_player
-        #   webview_flutter
-        # Deprecated; no plan to backfill the missing files:
-        #   android_intent,connectivity/connectivity,device_info/device_info,sensors,share,wifi_info_flutter/wifi_info_flutter
-        # No integration tests to run:
-        #   image_picker/image_picker - Native UI is the critical functionality
-        #   espresso - No Dart code, so no integration tests
-        PLUGINS_TO_EXCLUDE_INTEGRATION_TESTS: "camera/camera,google_sign_in/google_sign_in,in_app_purchase/in_app_purchase,in_app_purchase_android,quick_actions,shared_preferences/shared_preferences,url_launcher/url_launcher,video_player/video_player,webview_flutter,android_intent,connectivity/connectivity,device_info/device_info,sensors,share,wifi_info_flutter/wifi_info_flutter,image_picker/image_picker,espresso"
       build_script:
         # Unsetting CIRRUS_CHANGE_MESSAGE and CIRRUS_COMMIT_MESSAGE as they
         # might include non-ASCII characters which makes Gradle crash.
@@ -177,16 +161,13 @@
         - export CIRRUS_COMMIT_MESSAGE=""
         - if [[ -n "$GCLOUD_FIREBASE_TESTLAB_KEY" ]]; then
         -   echo $GCLOUD_FIREBASE_TESTLAB_KEY > ${HOME}/gcloud-service-key.json
-        -   ./script/tool_runner.sh firebase-test-lab --device model=flame,version=29 --device model=starqlteue,version=26 --exclude $PLUGINS_TO_EXCLUDE_INTEGRATION_TESTS
+        -   ./script/tool_runner.sh firebase-test-lab --device model=flame,version=29 --device model=starqlteue,version=26 --exclude=script/configs/exclude_integration_android.yaml
         - else
         -   echo "This user does not have permission to run Firebase Test Lab tests."
         - fi
     ### Web tasks ###
     - name: build-web+drive-examples
       env:
-        # Currently missing; see https://github.com/flutter/flutter/issues/81982
-        # and https://github.com/flutter/flutter/issues/82211
-        PLUGINS_TO_EXCLUDE_INTEGRATION_TESTS: "file_selector,shared_preferences_web"
         matrix:
           CHANNEL: "master"
           CHANNEL: "stable"
@@ -199,7 +180,7 @@
       build_script:
         - ./script/tool_runner.sh build-examples --web
       drive_script:
-        - ./script/tool_runner.sh drive-examples --web --exclude $PLUGINS_TO_EXCLUDE_INTEGRATION_TESTS
+        - ./script/tool_runner.sh drive-examples --web --exclude=script/configs/exclude_integration_web.yaml
 
 # macOS tasks.
 task:
@@ -221,10 +202,6 @@
     - name: build-ipas+drive-examples
       env:
         PATH: $PATH:/usr/local/bin
-        # in_app_purchase_ios is currently missing tests; see https://github.com/flutter/flutter/issues/81695
-        # ios_platform_images is currently missing tests; see https://github.com/flutter/flutter/issues/82208
-        # sensor hangs on CI.
-        PLUGINS_TO_EXCLUDE_INTEGRATION_TESTS: "in_app_purchase_ios,ios_platform_images,sensors"
         matrix:
           PLUGIN_SHARDING: "--shardIndex 0 --shardCount 4"
           PLUGIN_SHARDING: "--shardIndex 1 --shardCount 4"
@@ -247,7 +224,7 @@
         # `drive-examples` contains integration tests, which changes the UI of the application.
         # This UI change sometimes affects `xctest`.
         # So we run `drive-examples` after `native-test`; changing the order will result ci failure.
-        - ./script/tool_runner.sh drive-examples --ios --exclude $PLUGINS_TO_EXCLUDE_INTEGRATION_TESTS
+        - ./script/tool_runner.sh drive-examples --ios --exclude=script/configs/exclude_integration_ios.yaml
     ### macOS desktop tasks ###
     - name: build_all_plugins_macos
       env:
@@ -259,9 +236,6 @@
         - ./script/build_all_plugins_app.sh macos
     - name: build-macos+drive-examples
       env:
-        # conncectivity_macos is deprecated, so is not getting unit test backfill.
-        # package_info is deprecated, so is not getting unit test backfill.
-        PLUGINS_TO_EXCLUDE_MACOS_XCTESTS: "connectivity_macos,package_info"
         matrix:
           CHANNEL: "master"
           CHANNEL: "stable"
@@ -272,6 +246,6 @@
       xcode_analyze_script:
         - ./script/tool_runner.sh xcode-analyze --macos
       native_test_script:
-        - ./script/tool_runner.sh native-test --macos --exclude $PLUGINS_TO_EXCLUDE_MACOS_XCTESTS
+        - ./script/tool_runner.sh native-test --macos --exclude=script/configs/exclude_native_macos.yaml
       drive_script:
         - ./script/tool_runner.sh drive-examples --macos
diff --git a/packages/e2e/analysis_options.yaml b/packages/e2e/analysis_options.yaml
deleted file mode 100644
index cda4f6e..0000000
--- a/packages/e2e/analysis_options.yaml
+++ /dev/null
@@ -1 +0,0 @@
-include: ../../analysis_options_legacy.yaml
diff --git a/script/configs/README.md b/script/configs/README.md
new file mode 100644
index 0000000..96423cf
--- /dev/null
+++ b/script/configs/README.md
@@ -0,0 +1,8 @@
+This folder contains configuration files that are passed to commands in place
+of plugin lists. They are primarily used by CI to opt specific packages out of
+tests, but can also useful when running multi-plugin tests locally.
+
+**Any entry added to a file in this directory should include a comment**.
+Skipping tests or checks for plugins is usually not something we want to do,
+so should the comment should either include an issue link to the issue tracking
+removing it or—much more rarely—explaining why it is a permanent exclusion.
diff --git a/script/configs/custom_analysis.yaml b/script/configs/custom_analysis.yaml
new file mode 100644
index 0000000..f6dc8e2
--- /dev/null
+++ b/script/configs/custom_analysis.yaml
@@ -0,0 +1,41 @@
+# Plugins that deliberately use their own analysis_options.yaml.
+#
+# This only exists to allow incrementally switching to the newer, stricter
+# analysis_options.yaml based on flutter/flutter, rather than the original
+# rules based on pedantic (now at analysis_options_legacy.yaml).
+#
+# DO NOT add new entries to the list, unless it is to push the legacy rules
+# from a top-level package into more specific packages in order to incrementally
+# migrate a federated plugin.
+#
+# TODO(ecosystem): Remove everything from this list. See:
+# https://github.com/flutter/flutter/issues/76229
+- camera
+- file_selector
+- flutter_plugin_android_lifecycle
+- google_maps_flutter
+- google_sign_in
+- image_picker
+- in_app_purchase
+- integration_test
+- ios_platform_images
+- local_auth
+- plugin_platform_interface
+- quick_actions
+- shared_preferences
+- url_launcher
+- video_player
+- webview_flutter
+
+# These plugins are deprecated in favor of the Community Plus versions, and
+# will be removed from the repo once the critical support window has passed,
+# so are not worth updating.
+- android_alarm_manager
+- android_intent
+- battery
+- connectivity
+- device_info
+- package_info
+- sensors
+- share
+- wifi_info_flutter
diff --git a/script/configs/exclude_integration_android.yaml b/script/configs/exclude_integration_android.yaml
new file mode 100644
index 0000000..9fc31ec
--- /dev/null
+++ b/script/configs/exclude_integration_android.yaml
@@ -0,0 +1,22 @@
+# Currently missing harness files: https://github.com/flutter/flutter/issues/86749)
+- camera/camera
+- google_sign_in/google_sign_in
+- in_app_purchase/in_app_purchase
+- in_app_purchase_android
+- quick_actions
+- shared_preferences/shared_preferences
+- url_launcher/url_launcher
+- video_player/video_player
+- webview_flutter
+
+# Deprecated; no plan to backfill the missing files
+- android_intent
+- connectivity/connectivity
+- device_info/device_info
+- sensors
+- share
+- wifi_info_flutter/wifi_info_flutter
+
+# No integration tests to run:
+- image_picker/image_picker
+- espresso
diff --git a/script/configs/exclude_integration_ios.yaml b/script/configs/exclude_integration_ios.yaml
new file mode 100644
index 0000000..e1ae6ad
--- /dev/null
+++ b/script/configs/exclude_integration_ios.yaml
@@ -0,0 +1,6 @@
+# Currently missing: https://github.com/flutter/flutter/issues/81695
+- in_app_purchase_ios
+# Currently missing: https://github.com/flutter/flutter/issues/82208
+- ios_platform_images
+# Hangs on CI. Deprecated, so there is no plan to fix it.
+- sensors
diff --git a/script/configs/exclude_integration_web.yaml b/script/configs/exclude_integration_web.yaml
new file mode 100644
index 0000000..99e2083
--- /dev/null
+++ b/script/configs/exclude_integration_web.yaml
@@ -0,0 +1,4 @@
+# Currently missing: https://github.com/flutter/flutter/issues/81982
+- shared_preferences_web
+# Currently missing: https://github.com/flutter/flutter/issues/82211
+- file_selector
diff --git a/script/configs/exclude_native_macos.yaml b/script/configs/exclude_native_macos.yaml
new file mode 100644
index 0000000..8a817a9
--- /dev/null
+++ b/script/configs/exclude_native_macos.yaml
@@ -0,0 +1,3 @@
+# Deprecated plugins that will not be getting unit test backfill.
+- connectivity_macos
+- package_info
diff --git a/script/tool/CHANGELOG.md b/script/tool/CHANGELOG.md
index dc30c05..7d1eac0 100644
--- a/script/tool/CHANGELOG.md
+++ b/script/tool/CHANGELOG.md
@@ -1,5 +1,9 @@
 ## NEXT
 
+- `--exclude` and `--custom-analysis` now accept paths to YAML files that
+  contain lists of packages to exclude, in addition to just package names,
+  so that exclude lists can be maintained separately from scripts and CI
+  configuration.
 - Added an `xctest` flag to select specific test targets, to allow running only
   unit tests or integration tests.
 - **Breaking change**: Split Xcode analysis out of `xctest` and into a new
diff --git a/script/tool/lib/src/analyze_command.dart b/script/tool/lib/src/analyze_command.dart
index e56b95d..4fd15f0 100644
--- a/script/tool/lib/src/analyze_command.dart
+++ b/script/tool/lib/src/analyze_command.dart
@@ -6,6 +6,7 @@
 
 import 'package:file/file.dart';
 import 'package:platform/platform.dart';
+import 'package:yaml/yaml.dart';
 
 import 'common/core.dart';
 import 'common/package_looping_command.dart';
@@ -23,7 +24,10 @@
   }) : super(packagesDir, processRunner: processRunner, platform: platform) {
     argParser.addMultiOption(_customAnalysisFlag,
         help:
-            'Directories (comma separated) that are allowed to have their own analysis options.',
+            'Directories (comma separated) that are allowed to have their own '
+            'analysis options.\n\n'
+            'Alternately, a list of one or more YAML files that contain a list '
+            'of allowed directories.',
         defaultsTo: <String>[]);
     argParser.addOption(_analysisSdk,
         valueHelp: 'dart-sdk',
@@ -37,6 +41,8 @@
 
   late String _dartBinaryPath;
 
+  Set<String> _allowedCustomAnalysisDirectories = const <String>{};
+
   @override
   final String name = 'analyze';
 
@@ -56,7 +62,7 @@
         continue;
       }
 
-      final bool allowed = (getStringListArg(_customAnalysisFlag)).any(
+      final bool allowed = _allowedCustomAnalysisDirectories.any(
           (String directory) =>
               directory.isNotEmpty &&
               path.isWithin(
@@ -107,6 +113,17 @@
       throw ToolExit(_exitPackagesGetFailed);
     }
 
+    _allowedCustomAnalysisDirectories =
+        getStringListArg(_customAnalysisFlag).expand<String>((String item) {
+      if (item.endsWith('.yaml')) {
+        final File file = packagesDir.fileSystem.file(item);
+        return (loadYaml(file.readAsStringSync()) as YamlList)
+            .toList()
+            .cast<String>();
+      }
+      return <String>[item];
+    }).toSet();
+
     // Use the Dart SDK override if one was passed in.
     final String? dartSdk = argResults![_analysisSdk] as String?;
     _dartBinaryPath =
diff --git a/script/tool/lib/src/common/plugin_command.dart b/script/tool/lib/src/common/plugin_command.dart
index ecdcb05..7781eee 100644
--- a/script/tool/lib/src/common/plugin_command.dart
+++ b/script/tool/lib/src/common/plugin_command.dart
@@ -9,6 +9,7 @@
 import 'package:git/git.dart';
 import 'package:path/path.dart' as p;
 import 'package:platform/platform.dart';
+import 'package:yaml/yaml.dart';
 
 import 'core.dart';
 import 'git_version_finder.dart';
@@ -48,7 +49,9 @@
     argParser.addMultiOption(
       _excludeArg,
       abbr: 'e',
-      help: 'Exclude packages from this command.',
+      help: 'A list of packages to exclude from from this command.\n\n'
+          'Alternately, a list of one or more YAML files that contain a list '
+          'of packages to exclude.',
       defaultsTo: <String>[],
     );
     argParser.addFlag(_runOnChangedPackagesArg,
@@ -214,8 +217,18 @@
   ///    of packages in the flutter/packages repository.
   Stream<Directory> _getAllPlugins() async* {
     Set<String> plugins = Set<String>.from(getStringListArg(_packagesArg));
+
     final Set<String> excludedPlugins =
-        Set<String>.from(getStringListArg(_excludeArg));
+        getStringListArg(_excludeArg).expand<String>((String item) {
+      if (item.endsWith('.yaml')) {
+        final File file = packagesDir.fileSystem.file(item);
+        return (loadYaml(file.readAsStringSync()) as YamlList)
+            .toList()
+            .cast<String>();
+      }
+      return <String>[item];
+    }).toSet();
+
     final bool runOnChangedPackages = getBoolArg(_runOnChangedPackagesArg);
     if (plugins.isEmpty &&
         runOnChangedPackages &&
diff --git a/script/tool/test/analyze_command_test.dart b/script/tool/test/analyze_command_test.dart
index 69a2c4f..9dc8b6a 100644
--- a/script/tool/test/analyze_command_test.dart
+++ b/script/tool/test/analyze_command_test.dart
@@ -176,6 +176,25 @@
           ]));
     });
 
+    test('takes an allow config file', () async {
+      final Directory pluginDir = createFakePlugin('foo', packagesDir,
+          extraFiles: <String>['analysis_options.yaml']);
+      final File allowFile = packagesDir.childFile('custom.yaml');
+      allowFile.writeAsStringSync('- foo');
+
+      await runCapturingPrint(
+          runner, <String>['analyze', '--custom-analysis', allowFile.path]);
+
+      expect(
+          processRunner.recordedCalls,
+          orderedEquals(<ProcessCall>[
+            ProcessCall(
+                'flutter', const <String>['packages', 'get'], pluginDir.path),
+            ProcessCall('dart', const <String>['analyze', '--fatal-infos'],
+                pluginDir.path),
+          ]));
+    });
+
     // See: https://github.com/flutter/flutter/issues/78994
     test('takes an empty allow list', () async {
       createFakePlugin('foo', packagesDir,
diff --git a/script/tool/test/common/plugin_command_test.dart b/script/tool/test/common/plugin_command_test.dart
index fdab961..7f67acf 100644
--- a/script/tool/test/common/plugin_command_test.dart
+++ b/script/tool/test/common/plugin_command_test.dart
@@ -172,6 +172,19 @@
       expect(plugins, unorderedEquals(<String>[plugin2.path]));
     });
 
+    test('exclude accepts config files', () async {
+      createFakePlugin('plugin1', packagesDir);
+      final File configFile = packagesDir.childFile('exclude.yaml');
+      configFile.writeAsStringSync('- plugin1');
+
+      await runCapturingPrint(runner, <String>[
+        'sample',
+        '--packages=plugin1',
+        '--exclude=${configFile.path}'
+      ]);
+      expect(plugins, unorderedEquals(<String>[]));
+    });
+
     group('test run-on-changed-packages', () {
       test('all plugins should be tested if there are no changes.', () async {
         final Directory plugin1 = createFakePlugin('plugin1', packagesDir);
diff --git a/script/tool_runner.sh b/script/tool_runner.sh
index d16e940..11a54ce 100755
--- a/script/tool_runner.sh
+++ b/script/tool_runner.sh
@@ -10,58 +10,7 @@
 
 source "$SCRIPT_DIR/common.sh"
 
-# Plugins that are excluded from this task.
-ALL_EXCLUDED=("")
-
-# Plugins that deliberately use their own analysis_options.yaml.
-#
-# This list should only be deleted from, never added to. This only exists
-# because we adopted stricter analysis rules recently and needed to exclude
-# already failing packages to start linting the repo as a whole.
-#
-# Finding all: `find packages -name analysis_options.yaml | sort | cut -d/ -f2`
-#
-# TODO(ecosystem): Remove everything from this list. https://github.com/flutter/flutter/issues/76229
-CUSTOM_ANALYSIS_PLUGINS=(
-  android_alarm_manager
-  android_intent
-  battery
-  camera
-  connectivity
-  cross_file
-  device_info
-  e2e
-  espresso
-  file_selector
-  flutter_plugin_android_lifecycle
-  google_maps_flutter
-  google_sign_in
-  image_picker
-  in_app_purchase
-  integration_test
-  ios_platform_images
-  local_auth
-  package_info
-  plugin_platform_interface
-  quick_actions
-  sensors
-  share
-  shared_preferences
-  url_launcher
-  video_player
-  webview_flutter
-  wifi_info_flutter
-)
-
-# Comma-separated string of the list above
-readonly CUSTOM_FLAG=$(IFS=, ; echo "${CUSTOM_ANALYSIS_PLUGINS[*]}")
-# Set some default actions if run without arguments.
 ACTIONS=("$@")
-if [[ "${#ACTIONS[@]}" == 0 ]]; then
-  ACTIONS=("analyze" "--custom-analysis" "$CUSTOM_FLAG" "test" "java-test")
-elif [[ "${ACTIONS[0]}" == "analyze" ]]; then
-  ACTIONS=("${ACTIONS[@]}" "--custom-analysis" "$CUSTOM_FLAG")
-fi
 
 BRANCH_NAME="${BRANCH_NAME:-"$(git rev-parse --abbrev-ref HEAD)"}"
 
@@ -71,8 +20,8 @@
 
 if [[ "${BRANCH_NAME}" == "master" ]]; then
   echo "Running for all packages"
-  (cd "$REPO_DIR" && plugin_tools "${ACTIONS[@]}" --exclude="$ALL_EXCLUDED" ${PLUGIN_SHARDING[@]})
+  (cd "$REPO_DIR" && plugin_tools "${ACTIONS[@]}" ${PLUGIN_SHARDING[@]})
 else
   echo running "${ACTIONS[@]}"
-  (cd "$REPO_DIR" && plugin_tools "${ACTIONS[@]}" --run-on-changed-packages --exclude="$ALL_EXCLUDED" ${PLUGIN_SHARDING[@]})
+  (cd "$REPO_DIR" && plugin_tools "${ACTIONS[@]}" --run-on-changed-packages ${PLUGIN_SHARDING[@]})
 fi