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build: Make build copying more resilient
This fixes an issue where: 1. User tries to build before initializing all submodules. 2. `uplink-c` directory is empty and copied into build. 3. Build fails but leaves empty `uplink-c` directory in build directory 4. User initializes `uplink-c` and then tries to build again without cleaning. 5. `uplink-c` gets nested in a second level deeper, causing build issues.
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