Remove deprecated code from core (#2758)

* Remove parenthesized forms of:
`.unary_-()`, `.unary_%()`, `.unary_~()`, `.unary_!()`,
`.orR()`, `.andR()`, `.xorR()`,  `.zext()`, 
`.asBool()`, `.asBools()`, `.asSInt()`, `.asAsyncReset()`,
`.asClock()`, `.isLit()`, `.litOption()`, `.litValue()`,
`.abs()`
* Remove protected `Data.bindingToString`
* Remove `RawModule.getPorts`
* Remove `._applyMacroWithMessage` in assert and assume
* Remove `stop` that accepts non-zero return code
* Remove public `WhenContext` constructor
* Remove parenthesized `WhenContext.active()`
* Remove `blacklistPackages`, `builderName`, and `chiselStackTrace` from `ChiselException`
* Remove `MultiIOModule` (`Module` can have multiple `IOs`)
* Remove `chisel3.getModulePorts`
* Undo deprecation of `Data.flatten` which is package private and useful
* Also remove all internal uses of these removed methods

Co-authored-by: Jack Koenig <koenig@sifive.com>