When we use 'thmtools' package for creating 'List of Theorems', auxiliary file '.loe' is created, just as '.toc' for 'Table of Contents' and '.lof' for 'List of Figures'.

Latexian adds some additional temporary files, which are not required for building the project. Therefore they are better left out as well

A precompiled header(`latex -ini`) compiled creates a `.fmt` file.
To speed up xypic's drawing, precompiled matrices are created with the `\CompileMatrices` entry in the preamble. This creates `*.xyc` files.

[cprotect](https://www.ctan.org/tex-archive/macros/latex/contrib/cprotect?lang=en) tracks its contents in an auxiliary file, this is safe to ignore.

The pdfcomment package generates *.upa and *.upb files when compiling LaTeX files. These should be ignored as well.

endfloat.sty produces these two auxiliary files.
From Section 3.2 of its documentation:
> Loading it will have LTEX produce two extra files with .ttt and .fff extensions (for tables and figures, respectively).

As per http://tex.stackexchange.com/q/258515/828

TikZ uses *.auxlock files to check if the main *.aux file is available.
This is only used when using the external tikz library.

When using TikZ & PGF with:
`\usepackage{tikz} \usetikzlibrary{external} \tikzexternalize`
It creates .dpth and .md5 files for the externalized tikzpictures.

When using minitoc package, LateX often generates multiple .mtc files such as `*.mtc0`, `*.mtc1`, ..., `*.mtc13`, ... This patch allows one to ignore all *.mtc files from index 0 to index 99 (ignoring `*.mtc[1-9][0-9]`).

WinEdt (a popular TEX editor for windows) uses files "*.bak" for backup and "*.sav" for autosave.

*.synctex is generated when the synctex option is used under Windows.

Ignore acs-*.bib, an aux file generated by \documentclass{achemso} or by \usepackage{achemso}

When doing \usepackage[backref]{hyperref} the pages of the references are shown in the bibliography.
Those files can be safely ignored.

Info: http://tex.stackexchange.com/a/7772/828

To overcome the "No room for a new \write", the morewrites package (http://www.ctan.org/pkg/morewrites) uses a file with the .mw extension

This reverts commit 868789a441.

Sometimes it happens that you'd like to commit during a long LaTeX run. During this run, the document.synctex.gz is renamed to document.synctex.gz(busy). And you don't want to commit this file.

.brf files are generated if the 'backref' or 'pagebackref' options of the hyperref package are enabled. These are intermediate files, so shouldn't be tracked.

Refer to the biblatex manual at http://ctan.unsw.edu.au/macros/latex/contrib/biblatex/doc/biblatex.pdf:

(p.106): The name of the additional aux files is the base name of the main input file with the string -blx and a running number appended at the end.
[...]
Apart from these aux files, biblatex uses an additional bib file with the same suffix to pass certain control parameters to BibTeX.
[...]
When using Biber, biblatex writes a control file named example.bcf and ignores \blxauxsuffix.

Note: the running number mentioned in the documentation is not always added to the suffix.

From the man page for latexmk (http://manpages.ubuntu.com/manpages/raring/man1/latexmk.1L.html):

[...] the -recorder option with latex and pdflatex. In (most) modern versions of these programs, this results in a file of extension .fls containing a list of the files that these programs have read and written.

Latexmk specifies this option in its latex commands and so produces temporary files with this extension in latex projects.

See: http://tex.stackexchange.com/a/17846

The [todonotes package](http://www.tex.ac.uk/tex-archive/macros/latex/contrib/todonotes/todonotes.pdf)
generates "tdo" files when you use the \listoftodos command.