This changes a while the flash script, and updates the documentation
accordingly. It is a single commit because I couldn't test the script
until all changes were in place

Main changes:
  - fixed used interation: now it stops asking to remove the jumper
  - if "-b" is used and WRS_BASE_DIR is unset, defaults to current dir
  - all temporary files are in a specific directory, reported to the user
  - the script checks for the required files as first step, to err out soon
  - the 5-second sleep is removed, as there's an interactive step anyways
  - error messages are a little more verbose, to understand what was wrong
  - option parsing is more selective about flags for the flasher
Signed-off-by: Alessandro Rubini <rubini@gnudd.com>