Remove projectile-reindex-project

It was replaced with easier to use prefix arguments that force
cache invalidation for finding files and tests in a project.
Include untracked files in git ls-files's output.
Fix git ls-files arguments
Several improvements to the external commands backend

* more reliable VCS detection
* customizable external commands
* added a few missing docstring
Fix helm-projectile and optimize its performance
Add a simple version reporting command projectile-version.