Unable to apply SUPEE-6788 script... can I just use patch?

[ebtchad]

After a few days of tinkering with this issue I'm breaking down and asking the forum.

This is on a 1.9.0.1 install that I've personally installed all other patches on without any issue. I have full permissions. I don't fully understand everything that's going on in the top of the patch file.

My issue is basically that the patch script doesn't seem to do anything at all. I run it, the output doesn't suggest that anything happened, and Git doesn't show me anything that happened.

Output Follows:

vagrant@localdev:/var/www/mageroot$ sh PATCH_SUPEE-6788_CE_1.9.0.1_v1-2015-10-26-11-46-45.sh
PATCH_SUPEE-6788_CE_1.9.0.1_v1-2015-10-26-11-46-45.sh: 14: PATCH_SUPEE-6788_CE_1.9.0.1_v1-2015-10-26-11-46-45.sh: 127: not found
PATCH_SUPEE-6788_CE_1.9.0.1_v1-2015-10-26-11-46-45.sh: 14: PATCH_SUPEE-6788_CE_1.9.0.1_v1-2015-10-26-11-46-45.sh: 127: not found
PATCH_SUPEE-6788_CE_1.9.0.1_v1-2015-10-26-11-46-45.sh: 25: PATCH_SUPEE-6788_CE_1.9.0.1_v1-2015-10-26-11-46-45.sh: 0: not found
Checking if patch can be applied/reverted successfully...
-e ERROR: Patch can't be applied/reverted successfully.

checking file .htaccess
Hunk #1 FAILED at 207.
1 out of 1 hunk FAILED
checking file .htaccess.sample
Hunk #1 FAILED at 176.
1 out of 1 hunk FAILED
checking file app/code/core/Mage/Admin/Model/Block.php
checking file app/code/core/Mage/Admin/Model/Resource/Block.php
checking file app/code/core/Mage/Admin/Model/Resource/Block/Collection.php
checking file app/code/core/Mage/Admin/Model/Resource/Variable.php
checking file app/code/core/Mage/Admin/Model/Resource/Variable/Collection.php
checking file app/code/core/Mage/Admin/Model/Variable.php
checking file app/code/core/Mage/Admin/etc/config.xml
checking file app/code/core/Mage/Admin/sql/admin_setup/upgrade-1.6.1.1-1.6.1.2.php
checking file app/code/core/Mage/Adminhtml/Block/Permissions/Block.php
checking file app/code/core/Mage/Adminhtml/Block/Permissions/Block/Edit.php
checking file app/code/core/Mage/Adminhtml/Block/Permissions/Block/Edit/Form.php
checking file app/code/core/Mage/Adminhtml/Block/Permissions/Block/Grid.php
checking file app/code/core/Mage/Adminhtml/Block/Permissions/Variable.php
checking file app/code/core/Mage/Adminhtml/Block/Permissions/Variable/Edit.php
checking file app/code/core/Mage/Adminhtml/Block/Permissions/Variable/Edit/Form.php
checking file app/code/core/Mage/Adminhtml/Block/Permissions/Variable/Grid.php
checking file app/code/core/Mage/Adminhtml/controllers/Permissions/BlockController.php
checking file app/code/core/Mage/Adminhtml/controllers/Permissions/VariableController.php
checking file app/code/core/Mage/Adminhtml/etc/adminhtml.xml
checking file app/code/core/Mage/Catalog/Model/Product/Option/Type/File.php
checking file app/code/core/Mage/Core/Controller/Request/Http.php
checking file app/code/core/Mage/Core/Controller/Varien/Router/Admin.php
checking file app/code/core/Mage/Core/Helper/UnserializeArray.php
checking file app/code/core/Mage/Core/Model/Email/Template/Filter.php
checking file app/code/core/Mage/Core/Model/Resource/Setup.php
checking file app/code/core/Mage/Core/etc/config.xml
checking file app/code/core/Mage/Core/etc/system.xml
checking file app/code/core/Mage/Customer/Block/Account/Changeforgotten.php
checking file app/code/core/Mage/Customer/Block/Account/Resetpassword.php
checking file app/code/core/Mage/Customer/controllers/AccountController.php
checking file app/code/core/Mage/Downloadable/Model/Product/Type.php
checking file app/code/core/Mage/Eav/Model/Resource/Attribute/Collection.php
checking file app/code/core/Mage/Sales/Model/Resource/Order/Item/Collection.php
checking file app/code/core/Mage/Sales/controllers/DownloadController.php
checking file app/code/core/Mage/SalesRule/Model/Resource/Coupon/Collection.php
checking file app/code/core/Zend/Soap/Server.php
checking file app/code/core/Zend/Xml/Exception.php
checking file app/code/core/Zend/Xml/Security.php
checking file app/code/core/Zend/XmlRpc/Request.php
checking file app/code/core/Zend/XmlRpc/Response.php
checking file app/design/adminhtml/default/default/layout/admin.xml
checking file app/design/frontend/base/default/layout/customer.xml
checking file app/design/frontend/base/default/template/customer/form/register.phtml
checking file app/design/frontend/base/default/template/customer/form/resetforgottenpassword.phtml
checking file app/design/frontend/base/default/template/page/js/cookie.phtml
checking file app/design/frontend/base/default/template/persistent/customer/form/register.phtml
checking file app/design/frontend/default/iphone/layout/customer.xml
checking file app/design/frontend/default/modern/layout/customer.xml
checking file app/design/frontend/rwd/default/layout/customer.xml
checking file app/design/frontend/rwd/default/template/customer/form/resetforgottenpassword.phtml
checking file app/design/frontend/rwd/default/template/persistent/customer/form/register.phtml
checking file cron.php
checking file errors/processor.php
checking file lib/Unserialize/Parser.php
checking file lib/Unserialize/Reader/Arr.php
checking file lib/Unserialize/Reader/ArrKey.php
checking file lib/Unserialize/Reader/ArrValue.php
checking file lib/Unserialize/Reader/Bool.php
checking file lib/Unserialize/Reader/Dbl.php
checking file lib/Unserialize/Reader/Int.php
checking file lib/Unserialize/Reader/Str.php
checking file lib/Varien/Data/Collection/Db.php

However, in my troubleshooting I've tried just taking the patch's guts and applying it using "patch -p0 < patchguts.patch", which results in plenty of files being changed as I would expect. 

Is it ok to just patch it this way? One of my concerns is the lack of full information in the applied.patches.list. Is it important that all the patched files show up in there, or am I ok as long as I get the header line in there?

[ebtchad]

Aaaaand as soon as I posted this I tried just removing the .htaccess parts of the patch and it went through fine.

Maybe this will help someone else though. I'm all good now.

[iweb_p3mbo]

Hi,

The error is because you likely didn't have a .htaccess.sample file present. You say you have applied the patch now by removing the lines regarding the .htaccess files - however this file still needs to be patched.

You can do this manually by adding the following lines at the bottom of it:

###########################################
## Deny access to cron.php
    <Files cron.php>

############################################
## uncomment next lines to enable cron access with base HTTP authorization
## http://httpd.apache.org/docs/2.2/howto/auth.html
##
## Warning: .htpasswd file should be placed somewhere not accessible from the web.
## This is so that folks cannot download the password file.
## For example, if your documents are served out of /usr/local/apache/htdocs
## you might want to put the password file(s) in /usr/local/apache/.

        #AuthName "Cron auth"
        #AuthUserFile ../.htpasswd
        #AuthType basic
        #Require valid-user

############################################

        Order allow,deny
        Deny from all

    </Files>