Enh: logging and running

Sorry for a bit messy PR -- it also includes run_order PR which I have submitted earlier today.  Also it brings both non-functional changes for logging and some changes in how commands are ran in a single commit.  I still hope that someone would be able to review/merge.  Here are some details, but better just test it on your local "usecase" -- I hope you would enjoy current logging facility ;)

    Running --  Some kind of clean up must happen before every checkout, since some stale files
    might be in place and prevent a checkout.  In general cleaning up .py[co] might be
    insufficient if extensions are generated as well
    
    Logging -- coloring is enabled by default unless some of the in/out's doesn't have
    a TTY.  Seems to work quite neatly.  By default produces all the output, including
    DEBUG, but now much easier to parse.  Also added few more new logging messages.
    Timestamping is handy whenever the whole process hangs somewhere and it is desired
    to retrospect later on