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This is makeindex, version 2.15 [TeX Live 2012] (kpathsea + Thai support).
Scanning input file q...done (0 entries accepted, 2596 rejected).
Nothing written in q.ind.
Transcript written in q.ilg.
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This is makeindex, version 2.15 [TeX Live 2012] (kpathsea + Thai support).
Scanning input file p.idx....done (326 entries accepted, 1 rejected).
Sorting entries......done (3018 comparisons).
Generating output file p.ind....done (164 lines written, 0 warnings).
Output written in p.ind.
Transcript written in p.ilg.
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\indexentry{uha@\emph{ūha} (adaptation)}{x}
\indexentry{adesa@\emph{ādeśa} (substitute)}{1}
\indexentry{vikara@\emph{vikāra} (modification)}{2}
And so on. It is exactly identical to the p.idx file, although p.ilg is normal (whereas q.idg is quite wired, see below).
The preamble is quite long, but I tried to eliminate each of the packages one by one and this does not seem to make any difference. Moreover, the same preamble works fine with the index of version 'p'. Here is something closer to a MWE, omitting some packages and "makeatletter":
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\documentclass[14pt]{book}
\usepackage{fontspec}
\usepackage[english]{babel}
\usepackage{csquotes}
\usepackage{makeidx}
\usepackage{fancyhdr, blindtext}
\usepackage{hyphenat}
\usepackage{sectsty}
\usepackage{graphicx}
\usepackage{xcolor}
\usepackage[hang]{footmisc}
\footnotemargin1.8em
\makeindex
\author{}
\begin{document}
A minimal example of indexing\index{minimality} and a more complex one.\index{uha@\emph{ūha}}
\addcontentsline{toc}{chapter}{Index}
\printindex
\end{document}
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This is makeindex, version 2.15 [TeX Live 2012] (kpathsea + Thai support).
Scanning input file q...
!! Input index error (file = q, line = 1):
-- Unknown index keyword \documentclass[14pt].
!! Input index error (file = q, line = 2):
-- Unknown index keyword \usepackage.
!! Input index error (file = q, line = 3):
-- Unknown index keyword \usepackage[english].
!! Input index error (file = q, line = 4):
-- Unknown index keyword \usepackage.
!! Input index error (file = q, line = 5):
-- Unknown index keyword \usepackage.
!! Input index error (file = q, line = 6):
-- Unknown index keyword \usepackage.
!! Input index error (file = q, line = 7):
-- Unknown index keyword %\usepackage.
!! Input index error (file = q, line = 8):
-- Unknown index keyword \usepackage.
!! Input index error (file = q, line = 9):
-- Unknown index keyword \usepackage.
!! Input index error (file = q, line = 10):
-- Unknown index keyword \usepackage.
!! Input index error (file = q, line = 11):
-- Unknown index keyword \usepackage.
!! Input index error (file = q, line = 12):
-- Unknown index keyword %\usepackage.
!! Input index error (file = q, line = 14):
-- Unknown index keyword %\usepackage.
!! Input index error (file = q, line = 15):
-- Unknown index keyword %\deffootnote.
!! Input index error (file = q, line = 17):
-- Unknown index keyword \usepackage[hang].
!! Input index error (file = q, line = 18):
-- Missing arguments -- need two (premature LFD).
!! Input index error (file = q, line = 20):
-- Missing arguments -- need two (premature LFD).
!! Input index error (file = q, line = 21):[/quote]
And so on, including the text of the book itself, such as:[quote]
!! Input index error (file = tantra_s, line = 156):
-- Unknown index keyword Thepresentstudyisacompleteversionofthepreliminarystudythatappearedas\cite.
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!! Input index error (file = tantra_s, line = 3668):
-- Unknown index keyword \end.
done (0 entries accepted, 2596 rejected).
Nothing written in tantra_s.ind.
Transcript written in tantra_s.ilg.