Try Arara. It also has a great manual.
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Arara provides us with ways (rules) to compile the document that are specific the document. The rules for compilation are put inside the document. Hence, compilation boils down to a simple arara yourtexfile.
First, install arara and make sure that the arara executable is included in system path. To use arara we should add the rules inside the document itself:
% arara: pdflatex: {synctex: yes}
% arara: makeindex
% arara: biber
% arara: pdflatex: {synctex: yes}
% arara: pdflatex: {synctex: yes}
% arara: clean: {files: [arar-test.aux, arar-test.idx, arar-test.ilg, arar-test.ind, arar-test.log, arar-test.bbl, arar-test.bcf, arar-test.ist, arar-test.blg, arar-test.run.xml]}
%
\documentclass{article}
\usepackage[utf8]{inputenc}
\usepackage{filecontents}
\usepackage{makeidx}
\begin{filecontents}{\jobname.ist}
heading_prefix "{\\bfseries "
heading_suffix "\\hfil}\\nopagebreak\n"
headings_flag 1
delim_0 "\\dotfill "
delim_1 "\\dotfill "
delim_2 "\\dotfill "
delim_r "\\textendash"
suffix_2p "\\nohyperpage{\\,f.}"
suffix_3p "\\nohyperpage{\\,ff.}"
\end{filecontents}
\usepackage[backend=biber]{biblatex}
\addbibresource{biblatex-examples.bib}
\makeindex
\begin{document}
A citation\cite{companion} and an index entry\index{bla} and some arbitrary text.
\printbibliography
\printindex
\end{document}
To comment out an arara directive, just put ! like
% !arara: makeindex
For more details, consult the excellent arara guide.