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comment Overlapped appendices in Table of Contents
The iopart class does not make provisions for appendixes in the TOC. It will need a major rewrite of the \section, \l@section or both. The best advice is not to use a table of contents for IOP articles.
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comment how to cancel a space?
Inside a table environment look at Removing space in table with itemize environment
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comment providing a list of figure filenames used in tex file
Take a look at Create list of all external files used by master LaTeX document?