I can't install supee-8788, Magento versions is 1.9.2.3 CE. I will put here my applied.patches.list file.
in ssh I see something like this:
1 out of 1 hunk ignored -- saving rejects to file skin/adminhtml/default/default/media/uploader.swf.rej
patching file skin/adminhtml/default/default/media/uploaderSingle.swf
Reversed (or previously applied) patch detected! Assume -R? [n]
Apply anyway? [n]
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file skin/adminhtml/default/default/media/uploaderSingle.swf.rej
here is My file applied.patches.list
2016-01-05 20:20:06 UTC | SUPEE-5994 | CE_1.6.0.0 | v1 | _ | n/a | SUPEE-5994_CE_1.6.0.0_v1.patch
patching file app/code/core/Mage/Authorizenet/controllers/Directpost/PaymentController.php
patching file app/code/core/Mage/Core/Controller/Varien/Router/Admin.php
patching file app/code/core/Mage/Core/Controller/Varien/Router/Standard.php
patching file app/code/core/Mage/Customer/Model/Customer.php
patching file app/code/core/Mage/Dataflow/Model/Convert/Parser/Csv.php
patching file app/code/core/Mage/ImportExport/Model/Export/Adapter/Csv.php
patching file app/code/core/Mage/Install/Controller/Router/Install.php
patching file app/code/core/Mage/Install/etc/config.xml
patching file app/code/core/Mage/Sales/controllers/Recurring/ProfileController.php
patching file downloader/Maged/Model/Connect.php
patching file downloader/Maged/View.php
patching file downloader/template/connect/packages_prepare.phtml
patching file downloader/template/messages.phtml
patching file get.php
Hunk #1 succeeded at 36 (offset -1 lines).
patching file lib/PEAR/PEAR/PEAR.php
patching file lib/PEAR/PEAR/PEAR5.php
patching file lib/Varien/Io/File.php
2016-01-05 20:22:40 UTC | SUPEE-6285 | CE_1.9.1.1 | v2 | 7226d88b1eeb07a5fbc4e62be189a5219457cc14 | Mon Jun 22 16:32:26 2015 +0300 | 202596e441..7226d88b1e
patching file app/Mage.php
patching file app/code/community/Phoenix/Moneybookers/controllers/MoneybookersController.php
patching file app/code/core/Mage/Adminhtml/Controller/Action.php
patching file app/code/core/Mage/Adminhtml/controllers/AjaxController.php
patching file app/code/core/Mage/Adminhtml/controllers/Catalog/Category/WidgetController.php
patching file app/code/core/Mage/Adminhtml/controllers/Catalog/Product/DatafeedsController.php
patching file app/code/core/Mage/Adminhtml/controllers/Catalog/Product/ReviewController.php
patching file app/code/core/Mage/Adminhtml/controllers/Catalog/Product/WidgetController.php
patching file app/code/core/Mage/Adminhtml/controllers/Cms/Block/WidgetController.php
patching file app/code/core/Mage/Adminhtml/controllers/Cms/Page/WidgetController.php
patching file app/code/core/Mage/Adminhtml/controllers/Cms/PageController.php
patching file app/code/core/Mage/Adminhtml/controllers/Cms/WysiwygController.php
patching file app/code/core/Mage/Adminhtml/controllers/Customer/System/Config/ValidatevatController.php
patching file app/code/core/Mage/Adminhtml/controllers/JsonController.php
patching file app/code/core/Mage/Adminhtml/controllers/NotificationController.php
patching file app/code/core/Mage/Adminhtml/controllers/Report/CustomerController.php
patching file app/code/core/Mage/Adminhtml/controllers/Report/ProductController.php
patching file app/code/core/Mage/Adminhtml/controllers/Report/ReviewController.php
patching file app/code/core/Mage/Adminhtml/controllers/Report/SalesController.php
patching file app/code/core/Mage/Adminhtml/controllers/Report/ShopcartController.php
patching file app/code/core/Mage/Adminhtml/controllers/Report/TagController.php
patching file app/code/core/Mage/Adminhtml/controllers/ReportController.php
patching file app/code/core/Mage/Adminhtml/controllers/Rss/CatalogController.php
patching file app/code/core/Mage/Adminhtml/controllers/Rss/OrderController.php
patching file app/code/core/Mage/Adminhtml/controllers/Sales/Billing/AgreementController.php
patching file app/code/core/Mage/Adminhtml/controllers/Sales/Order/View/GiftmessageController.php
patching file app/code/core/Mage/Adminhtml/controllers/Sales/Recurring/ProfileController.php
patching file app/code/core/Mage/Adminhtml/controllers/Sales/TransactionsController.php
patching file app/code/core/Mage/Adminhtml/controllers/System/Config/System/StorageController.php
patching file app/code/core/Mage/Adminhtml/controllers/TagController.php
patching file app/code/core/Mage/Adminhtml/controllers/Tax/RateController.php
patching file app/code/core/Mage/Adminhtml/controllers/TaxController.php
patching file app/code/core/Mage/Api2/controllers/Adminhtml/Api2/AttributeController.php
patching file app/code/core/Mage/Bundle/controllers/Adminhtml/Bundle/SelectionController.php
patching file app/code/core/Mage/Captcha/controllers/Adminhtml/RefreshController.php
patching file app/code/core/Mage/Centinel/controllers/Adminhtml/Centinel/IndexController.php
patching file app/code/core/Mage/Checkout/controllers/MultishippingController.php
patching file app/code/core/Mage/Connect/controllers/Adminhtml/Extension/LocalController.php
patching file app/code/core/Mage/ImportExport/Model/Abstract.php
patching file app/code/core/Mage/Oauth/controllers/Adminhtml/Oauth/AuthorizeController.php
patching file app/code/core/Mage/Paygate/controllers/Adminhtml/Paygate/Authorizenet/PaymentController.php
patching file app/code/core/Mage/Paypal/controllers/Adminhtml/Paypal/ReportsController.php
patching file app/code/core/Mage/Rss/controllers/CatalogController.php
patching file app/code/core/Mage/Rss/controllers/OrderController.php
patching file app/code/core/Mage/Widget/Block/Adminhtml/Widget/Chooser.php
patching file app/code/core/Mage/Widget/controllers/Adminhtml/WidgetController.php
patching file app/design/frontend/base/default/template/checkout/cart.phtml
patching file app/design/frontend/base/default/template/checkout/cart/noItems.phtml
patching file app/design/frontend/base/default/template/checkout/onepage/failure.phtml
patching file app/design/frontend/base/default/template/rss/order/details.phtml
patching file app/design/frontend/base/default/template/wishlist/email/rss.phtml
patching file app/design/frontend/default/modern/template/checkout/cart.phtml
patching file app/design/frontend/rwd/default/template/checkout/cart.phtml
patching file downloader/Maged/.htaccess
patching file downloader/Maged/Controller.php
patching file downloader/Maged/Model/Session.php
patching file downloader/lib/.htaccess
patching file downloader/template/connect/packages.phtml
patching file downloader/template/connect/packages_prepare.phtml
patching file downloader/template/login.phtml
patching file downloader/template/settings.phtml
patching file errors/processor.php
2016-01-05 20:24:06 UTC | SUPEE-6482 | CE_1.9.2.0 | v1 | | Tue Jul 14 14:17:04 2015 +0300 |
patching file app/code/core/Mage/Api/Model/Server/Adapter/Soap.php
Hunk #1 succeeded at 209 (offset -24 lines).
patching file app/code/core/Mage/Catalog/Model/Product/Api/V2.php
2017-02-06 11:55:18 UTC | SUPEE-1533 | EE_1.13 | v1 | _ | n/a | SUPEE-1533_EE_1.13_v1.patch | REVERTED
patching file app/code/core/Mage/Adminhtml/Block/Dashboard/Graph.php
patching file app/code/core/Mage/Adminhtml/controllers/DashboardController.php
.sh
so i tried with FTP (direct file upload) and it works for me