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.
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