First set right permission to your source code files. Second if hacker have access to your computer through a rootkit or backdoor, he can do anything with your machine, even manipulating spyware detection or antivirus softwares. So better keep the file set encrypted on your harddisk. NTFS provides that future.
Anyways when you will publish your software, if its really good, people ll find out its source code using reverse engineering..
so dont think much beyond setting some security measures.