There are a few major elements.
1) Nuclear processing facilities are huge, specific and complex. A lot of the equipment can’t easily be moved. They tend to have limited use beyond nuclear weapons processing and it takes a long time to assemble and disassemble stuff.
2) They try to make the inspections with as little notice as possible.
3) There are some information sources we can access at any time. Those can tell us a lot about a facility too. Trucks, financial transactions, shipping manifests can provide further evidence.
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