A problem with \newcommand
I found a problem with \newcommand.
a.tex :
\begin{document}
\newcommand{\beq}{\begin{eqnarray}}
\newcommand{\eeq}{\end{eqnarray}}
\beq
e^{i\pi} + 1 = 0.
\eeq
\end{document}
latexdiff a.tex a.tex > diff.tex gives the following diff.tex :
\begin{document}
\newcommand{\beq}{\begin{eqnarray}\end{eqnarray}
\newcommand{\eeq}{}}
\beq
e^{i\pi} + 1 = 0.
\eeq
\end{document}
This is a a somewhat pathological case. You can fix this by moving the definitions into the preamble I think. Even if this wrong processing was fixed, latexdiff would still not understand \beq and \eeq as math delimiters, likely leading to problems if equations get more complex. To fix this somehow the content of \newcommand's needs to be protected against pre-processing - not really difficult to do but still taking some time. Because of the above mentioned workaround and remaining issues even after a fix for this construction I am currently not planning to implement this but will leave the issue open.