The latest version (available on github) contains a switch, -c=/path/to/cruft/directory that performs in the way you described. You can use it as follows, for example
latexindent.pl -w -c=/home/cmhughes/Desktop myfile.tex
which will output all of the 'cruft' (indent.log, myfile.bak*) to /home/cmhughes/Desktop. It performs a check to make sure that the directory exists- if it doesn't, then the script will exit.
I did think about implementing this in the yaml files, but since indent.log writes information about the contents of these files, I found myself going round in circles. As such, the suggestion to use a command line switch makes the most sense.
I have also updated the arara rule which can be used as, for example,
% arara: indent: { cruft: /home/cmhughes/Desktop }
I have found the arara rule does not like it when the directories contain spaces (but the command line version doesn't mind).
pdflatex: LaTeX Editing Using Notepad++, besides of course this one on TeX.SX: http://tex.stackexchange.com/questions/43984/using-notepad-with-miktex-on-windows – Herr K. Nov 06 '13 at 20:03latexindent! That's a great idea; it's not currently possible, but I'll add it to the to-do list. Presumably you would want to specify the settings in ayamlfile with switches (something like):backupDirectory: /my/output/directoryandlogfileDirectory: /some/other/directory? – cmhughes Nov 06 '13 at 20:20-output-directory=<folder>does inpdflatex; for example, as inlatexindent.pl -w -output-directory=<path to folder> foo.tex. I suppose this will imply a change in the.plfile (but I'm not sure). Settings in ayamlfile would imply that all backup and log files will be saved in those same folder(s) regardless of wherefoo.texwas initially saved, right? – Herr K. Nov 06 '13 at 22:01yamlfiles- you havedefaultSettings.yaml, and then your own files which can reside anywhere; in particular, you can havelocalSettings.yamlwhich overrides anything else. Most of the script's behaviour is controlled fromyaml, so my first instinct is to put it in there. I hope to get to the to-do list at some point soon.... – cmhughes Nov 07 '13 at 00:04latexindent:)– Herr K. Nov 07 '13 at 00:32