Separate installation into two distinct sections

The existing README is not particularly well suited to people who
actually want to *use* a script repository rather than create their own
scripts via their own GitHub fork.  This commit improves that.

An HTTPS clone URL is also used for the user installation section.  This
URL is actually usable in a systems administration context where the
installation environment is not registered with GitHub.
Make (3) more readable
Revert "Make (3) more readable"

This reverts commit 12ebf7aef8daba87d885f132f6df100e4c48dcd2.
Add some more verbiage to (3)
Add an upgrading section
Be a bit more thorough with explaining directory names
Merge pull request #5 from chris-allan/install-separation

Install separation
Merge remote-tracking branch 'openmicroscopy/master' into readme-from-upstream
Merge pull request #4 from chris-allan/readme-from-upstream

Readme from upstream