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I note that AUCTeX calls makeindex without file extension, e.g., makeindex tmp instead of makeindex tmp.idx. It means if there is a subdirectory with the same name as the first part of the file name makeindex does not see the .idx file producing and empty .ind file. Is that a bug or a feature? Shouldn't AUCTeX call makeindex with the file extension?

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If you want to change the call just sometimes, you can issue C-u C-c C-c Index RET (note the prefix argument C-u before the usual C-c C-c) and then add on the command line the extension.

If instead you want to always change how AUCTeX runs makeindex, you can either customize the Index entry of TeX-command-list variable with M-x customize-variable RET TeX-command-list RET and replace %s with %s.idx in the Command field, or add the following code to your init file (this is the same as doing what I've said before but with just copy-&-paste)

(eval-after-load "tex"
  '(add-to-list 'TeX-command-list '("Index" "makeindex %s.idx" TeX-run-index nil t
                    :help "Run makeindex to create index file")))
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