rewrite run_command and correct its usage
packaging
Merge pull request #3 from driquet/rewrite_process

Rewrite process
adding init
Made cleaning function more robust
Added --no-pdf flag and made generated files live in same folder as source file.
Made destination folder robust to relative paths
Added the option of running pdflatex. Improved cleaning.
Added the option of opening pdf in native viewer
Added ability to diff with current working copy. Also added more help text.
Merge pull request #4 from ihincks/master

What a great job @lhincks !
You did a wonderful job by adding these features, thank you a lot !
Merged upstream changes