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Minor change. If module was installed in "sites/default/modules/flot" the library would not be found when using the make file. Since flot will look in sites/all/libraries is the Library API is installed, the make file will use that.
The Flot module for Drupal 8 has been upgraded to beta. Do not expect any API changes in the 1.0 branch going forward. There has been one large change since the alpha stage, and that is the primary twig template was renamed from flot-my-template to flot-element. If your installation had a custom twig template that extended the original template, you will have to change the name.
First stable version for Drupal 7, the main module contains the API and theme functions. Flot views is the integration with views (dependency: http://drupal.org/project/views_decorator) and contains a new (prefered) views style plugin to create flot graphs, Flot fields.
The old views integration using Flot Datapoint is deprecated, it might work, but it will not receive any new features.