Permitting LaTeX to execute shell code (aka -enable-write-18) is dangerous. But I sometimes need it due to dot2texi. So in my IDE (which in my case is WinEdt) I manually switch it on when I work with dot2texi, and switch it off when when I do not longer work with dot2texi AND (important) do not forget it (weak spot). I vaguely recall that switching on shell escapes can be done as per document. That would be nice. Does anyone remember how?
For example, to get the citation right, you normally need to run
Because this is a lot of typing exercise in your terminal, or a lot of keystrokes in your editor, there is
and then run
You can also add further options to the single tasks, like shell escape:
For more info read the magnificent documentation, or see this tutorial on texdev.net: http://www.texdev.net/2012/04/24/arara-making-latex-files-your-way/
With TeXworks magic comments you can set typesetting engine, encoding, etc. Here an example: