But do Lua source files specify which version of Lua they use, by some marker in the file? by file extension? If not how would the specific filetype be chosen when a file is opened?

The lua version is not included in the script. (An exception is a file with a shebang, but such a file is uncommon and can only be executed directly and not included with dofile.)

Most other languages highlight all keywords of all versions, but many of them only add keywords not remove keywords, Lua would be unusual in removing them.

I assume that for consistency it should also highlight old keywords and my changes are too simple.

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