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The C part of Emacs is portable to C89: C99-specific features such as ‘<stdbool.h>’ and ‘inline’ are not used without a check, typically at configuration time, and the Emacs build procedure provides a substitute implementation if necessary. Some C99 features, such as declarations after statements, are too difficult to provide substitutes for, so they are avoided entirely.
At some point in the not-too-distant future the base C dialect will change from C89 to C99, and eventually it will no doubt change to C11.