I suspect you have a directory structure, something like:
folder1/ text.txt level1/ text1.txt level2/ text2.txt level3/ text3.txt folder2 text.txt level1/ text1.txt level2/ text2.txt anewdirectory/ newtext.txt level3/ text3.txt newfiled3.txt
In this case, diff will ignore the newtext.txt file inside anewdirectory/ . It probably also does not display the text newfiled3.txt . Instead, it reports something like:
.. Only in folder2/level1/level2/ : anewdirectory Only in folder2/level1/level2/level3/ : newfiled3.txt ..
Is this a symptom that you see?
Try:
diff -urBNs folder1/ folder2/ > code.patch
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