Question: I want to start writing on an article that is probably going to be published in one of the IOP journals. There is a template for their publications, but it lacks some (for me) essential packages. Since I've never submitted an article myself, I want to be sure the editing process goes as smooth as possible by eliminating problems early. So here's the question:

Can I add all the packages I like to the template without pissing off the editor? I talk about things like `inputenc`, `fontenc`, `biblatex`, `microtype`, etc. Nothing fancy, but very basic LaTeX stuff. I also prefer to have a separate `.bib` file for my bibliography, since I have them already organized that way and do not want to manually copy the info into the bibliography as suggested in the template.

I already read the guidelines for authors and there was no mention of modifying the template, only that its use is highly appreciated. 

If anyone could provide any (preferrably inside info) on how editors work with submitted LaTeX files, that would help a lot! Thanks.

Answer: 
Unless explicitly forbidden, adding packages is usually ok and fully expected - e.g. in order to add support for listings, tables, symbols, encodings, operational utilities (extended macro/logic support), or specific features thereof. This should, however, never mean a general change in the appearance of the paper. Therefore, packages that globally alter fonts or font sizes are usually not allowed.

As for using a separate `.bib` file, you can usually work with that and (if explicitly requested by the guidelines - this varies a lot by publisher) copy the formatted information into the `.tex` file as late as for the camera-ready version (when nothing changes any more).
I usually publish in IOP journals and I can confirm [O. R. Mapper's](https://academia.stackexchange.com/a/73074/20058) remarks.

As an example, these are the packages included in a recent paper of mine:

```
\documentclass[10pt,a4paper]{iopart}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{iopams}
\usepackage{amsopn}
\usepackage{graphicx}
\usepackage{cite}
\usepackage{siunitx}
\usepackage{tikz}
\usepackage{array}
\usepackage{subfigure}
\usepackage{longtable}
\usepackage{listings}

```

Notice that for what concerns mathematics, there are a few idiosyncrasies related to the `iopart` class: e.g., this class is incompatible with the `amsmath` package, and it is suggested to use the `eqnarray` environment, which is otherwise deprecated. I thus suggest a careful reading of the IOP LaTeX guidelines, which can be found [here](ftp://ftp.iop.org/pub/journals/latex2e/IOPLaTeXGuidelines.pdf).

A few notes on the example above:

* The package `iopams` is an extension for `amssymb` to provide
predefined names for bold greek letters (thanks to Barbara Beeton for
pointing out this and Canageek for reporting it here).
* The package `subfigure` is obsolete but the the newer `subfig` package seems to be incompatible with `iopart` because it includes the `caption` package.