Note: This issue appears to apply to all versions of Magento which received the SUPEE-6788 patch. You'll see in my answer that both .htaccess and .htaccess.sample need to be restored for the patch to succeed.
I'm working on applying the SUPEE-6788 patch to a CE 1.7.0.2 site using the shell script provided by magentocommerce.com/downloads. The site has had all previous security patches applied.
The script's name is PATCH_SUPEE-6788_CE_1.7.0.2_v1-2015-10-27-12-00-16.sh and has an md5sum of cfc0cf533fe36a5f573414f0feeb1590 (this patch was unusual in that it was released uncompressed–although the file doesn't appear corrupt or truncated).
When running this script the console output appears to indicate that at least one of the included patches failed or was skipped, but that many parts of the patch were successful, however git is showing no changes. The script has been tested on two different environments with the same codebase--one an Ubuntu GNOME 14.04 LTS workstation, the other a nexcess.com shared server (running CentOS).
Of interest is that the output on the two environments is slightly different. Note the lines starting with "checking" vs "patching".
A sample of output from the Ubuntu environment:
bash PATCH_SUPEE-6788_CE_1.7.0.2_v1-2015-10-27-12-00-16.sh [19:27:10]
Checking if patch can be applied/reverted successfully...
ERROR: Patch can't be applied/reverted successfully.
checking file .htaccess
Hunk #1 FAILED at 207.
1 out of 1 hunk FAILED
can't find file to patch at input line 38
Perhaps you used the wrong -p or --strip option?
The text leading up to this was:
--------------------------
|diff --git .htaccess.sample .htaccess.sample
|index 546f18e..3e79c77 100644
|--- .htaccess.sample
|+++ .htaccess.sample
--------------------------
File to patch:
Skip this patch? [y]
Skipping patch.
1 out of 1 hunk ignored
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
...
A sample from the CentOS environment:
bash PATCH_SUPEE-6788_CE_1.7.0.2_v1-2015-10-27-12-00-16.sh
Checking if patch can be applied/reverted successfully...
ERROR: Patch can't be applied/reverted successfully.
patching file .htaccess
Hunk #1 FAILED at 207.
1 out of 1 hunk FAILED -- saving rejects to file .htaccess.rej
can't find file to patch at input line 38
Perhaps you used the wrong -p or --strip option?
The text leading up to this was:
--------------------------
|diff --git .htaccess.sample .htaccess.sample
|index 546f18e..3e79c77 100644
|--- .htaccess.sample
|+++ .htaccess.sample
--------------------------
File to patch:
Skip this patch? [y]
Skipping patch.
1 out of 1 hunk ignored
patching file app/code/core/Mage/Admin/Model/Block.php
patching file app/code/core/Mage/Admin/Model/Resource/Block.php
patching file app/code/core/Mage/Admin/Model/Resource/Block/Collection.php
patching file app/code/core/Mage/Admin/Model/Resource/Variable.php
...
I'll be digging into the error at the top of the output and possible manually applying the patches--but was hoping that someone might have insight into the cause or a relatively simple fix.