Deprecated and slated for 2.0 removal

[IAlibay]

We have quite a lot of things that are slated for removal in 2.0:

• old density code Removes deprecated density code #2740
• old hole code Remove deprecated hole, and completes py2 removal #2778
• old hbonds code Remove deprecated hbonds.hbond_analysis #2746
• deprecated writers Timestep code Remove ts from writers #2754
• progressmeter Remove ProgressMeter #2743

With #2729 I guess we started 2.0 a little bit sooner than anticipated, so I thought I'd check that we are good at doing these removals before we go ahead and start cutting out code?

[orbeckst]

Let‘s get started. We‘ll have to figure out a way to do patches for 1.0 but it seems we can just do PRs against master at the moment and treat master as 1.x branch.

We‘ll figure out a way to backport fixes from develop; I assume that if we do squash merges we get fairly clean diffs that we can cherry-pick or merge into master/1.x.

[orbeckst]

Also: remove six!