PrimeIntellect/SWE-rebench-V2 huggingface dataset:
Repository: symfony/flex (php)

Issue:
DiffHelper corrups patches when removing the last file
When the last file of a patch is removed, the patch final eol is also removed.

A patch without a final eol is reported as corrupted by `git` (tested 2.25.1 from Ubuntu 20.04 and 2.35.0 from Ubuntu PPA).

I pushed a reproducer: https://github.com/fbourigault/flex-update-doctrine-bundle-recipe

The reproducer is a Symfony 4.4 on PHP 7.4 with `doctrine/doctrine-bundle` `2.3` applied and `config/packages/test/doctrine.yaml` file removed. The `doctrine/doctrine-bundle` recipe is ready to be updated.

Pull request:
Fixing missing blank line at end of modified patch files
Fixes #856

tl;dr If a file has been modified in a recipe, but that file has been deleted in the user's project, we manually remove that file from that patch to avoid conflicts (and we report the patch to the user). There was a bug in that process that didn't guarantee an empty line at the end of the patch file. That made the patch file invalid for git.

Thank you @fbourigault for the excellent bug report and reproducer!

Patch:
diff --git a/src/Update/DiffHelper.php b/src/Update/DiffHelper.php
index 4e037de..7072889 100644
--- a/src/Update/DiffHelper.php
+++ b/src/Update/DiffHelper.php
@@ -35,6 +35,11 @@ class DiffHelper
             $patch = $contentBefore.substr($patch, $end);
         }
 
+        // valid patches end with a blank line
+        if ($patch && "\n" !== substr($patch, \strlen($patch) - 1, 1)) {
+            $patch = $patch."\n";
+        }
+
         return $patch;
     }
 }


Test patch:
diff --git a/tests/Update/DiffHelperTest.php b/tests/Update/DiffHelperTest.php
index 9441f6d..5ee9760 100644
--- a/tests/Update/DiffHelperTest.php
+++ b/tests/Update/DiffHelperTest.php
@@ -105,6 +105,7 @@ index 0000000..34c2ebc
 +    dbal:
 +        # "TEST_TOKEN" is typically set by ParaTest
 +        dbname_suffix: '_test%env(default::TEST_TOKEN)%'
+
 EOF
             , [
                 '.env' => <<<EOF
@@ -154,6 +155,7 @@ index 0000000..34c2ebc
 +    dbal:
 +        # "TEST_TOKEN" is typically set by ParaTest
 +        dbname_suffix: '_test%env(default::TEST_TOKEN)%'
+
 EOF
             , [
                 'config/packages/doctrine.yaml' => <<<EOF
@@ -204,6 +206,7 @@ index 8ae31a3..17299e2 100644
 -            type: pool
 -            pool: doctrine.system_cache_pool
          query_cache_driver:
+
 EOF
             , [
                 'config/packages/test/doctrine.yaml' => <<<EOF
@@ -244,6 +247,7 @@ index 8ae31a3..17299e2 100644
 -            type: pool
 -            pool: doctrine.system_cache_pool
          query_cache_driver:
+
 EOF
             , [
                 'config/packages/test/doctrine.yaml' => <<<EOF