**I'm assuming code is referring collectively to all the pieces of coding in files SVN and Test case document.
In this sentence:
"Code in SVN and Test case document is updated accordingly."
the code is being updated, which is present in the files SVN and Test case document. Since 'code' is singular, you should use 'is', not 'are'.
We aren't referring to the SVN and TCD while talking about the updating. That is only to do with the code. So we check out the plurality by seeing 'code'.
Even if your sentence were, say:
"The code in all the files has been updated."
Even though 'files' is plural, it is the singular 'code' which is being updated. This is why we use 'has been updated' (which is used for singular) rather than 'have been updated' (which would have been used in case of plural).
Check out this sentence:
"The Java codes in the file are being updated."
Over here, we've used 'are' because the update is happening to the Java codes, which is plural. Even though the word just before 'are' is singular (file).