[Cil] Replace theMachine by the new Machine module

src/kernel_internals/parsing/clexer.mll

src/kernel_internals/parsing/cparser.mly

src/kernel_internals/runtime/special_hooks.ml

src/kernel_internals/typing/cabs2cil.ml

src/kernel_internals/typing/rmtmps.ml

src/kernel_services/abstract_interp/base.ml

src/kernel_services/abstract_interp/cvalue.ml

src/kernel_services/abstract_interp/offsetmap.ml

src/kernel_services/analysis/bit_utils.ml

src/kernel_services/analysis/destructors.ml

src/kernel_services/ast_data/alarms.ml

src/kernel_services/ast_data/ast.ml

src/kernel_services/ast_data/cil_types.ml

src/kernel_services/ast_printing/cil_printer.ml

src/kernel_services/ast_queries/cil.ml

src/kernel_services/ast_queries/cil.mli

src/kernel_services/ast_queries/cil_builtins.ml

src/kernel_services/ast_queries/cil_builtins.mli

src/kernel_services/ast_queries/file.ml

src/kernel_services/ast_queries/logic_typing.ml