[LLVMdev] LLD: make atoms in files non-const

[Rui Ueyama]

Currently, member functions like File::defined() return an iterator for
const atoms. But we don't actually treat atoms as consts -- we updates
atoms in many places including the core resolver.

We have too many const_casts in our code. It just doesn't make sense.

I'm making a change to make atoms non-const. Please hit reply if you have
any concerns.
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