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1. Now you can use "Meld tool" to compare between files to refresh the patch. Here you can compare between the source file generated in step 2 (which will have the required changes) and the source file generated in step-3 (which will have the patch appied on to it).
2. During comparing between source files make sure that you take only the required changes (changes available in actual source file step-2) to the patched file generated in step-3.
3. Once all changes are taken , you can verify the patch by checking the option file/format as patch in the tool. Save the updated file and copy it to your repo (repo generated in step-2).
4. Now in your repo , you will have 2 source file (for ex: one will be index.php --original file with the required changes and index_bk.php --updated file with patch applied and also your changes).
5. In terminal , you can use command "diff -ruN  file1 file2 > new_patch_file.patch" to generate a  new patch.
6. For ex : diff -ruN index.php index_bk.php > new_index.patch
7. In case patch file has more than one file, then append the difference using diff -ruN next_file nextfile_bk.php >> new_index.patch

Step 5 :

1. Open the newly created patch file, update the file location correctly and save it. For ex :

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