Remove legacy h5py based formats

[benjeffery]

Opening this up for discussion.

As mentioned by @jeromekelleher at #2811 (comment) it has been a long time since these legacy formats were used. When dropping them we should add a note in the docs to specify the version of tskit to use to upgrade the file.

[jeromekelleher]

Agree. We should add a stable hyperlink on the tskit docs (Legacy HDF5 file formats) which we provide a link to in the error message also, so people know where to look when the file doesn't load.

[molpopgen]

I think we should do this ASAP. Definitely want to get it out of the way before any kind of 1.0 release is on the horizon.

[jeromekelleher]

I might just go ahead and do this, we've got a bunch of PRs in flight and #2811 doesn't look like a quick fix. Any objections @benjeffery?

[benjeffery]

#2811 needs to be done for lshmm anyway. So expediting this won't help. I should get #2811done today.

[jeromekelleher]

Ah right, let's backburner so

[benjeffery]

Fixed in #3138