API changes: particlefile.py and other touchups

[VeckoTheGecko]

Contributes to #1695

Changes

• API changes

---

This PR makes many of the names in particlefile.py (and some other files):

• private - in the case where users are not expected to use them (attributes and methods),
• read only where edits to said variables would provide unexpected behaviour/side effects (attributes), or
• removed (where they are either legacy code, or there are better mechanisms to achieve the same result)

All privatisations/removals are done in a non-breaking way, raising a deprecation warning.

The method/attributes affected are:

Class	Method/Attribute	Action
ParticleSet	iterator()	remove
ParticleData	iterator()	remove
ParticleFile	add_metadata()	remove
ParticleFile	write_once()	make_private
ParticleFile	create_new_zarrfile	read_only
ParticleFile	outputdt	read_only
ParticleFile	chunks	read_only
ParticleFile	particleset	read_only
ParticleFile	fname	read_only
ParticleFile	vars_to_write	read_only
ParticleFile	time_origin	read_only
ParticleFile	parcels_mesh	make_private
ParticleFile	maxids	make_private
ParticleFile	pids_written	make_private
ParticleFile	mpi_rank	make_private
ParticleFile	fill_value_map	make_private
ParticleFile	analytical	make_private (+rename)
Grid	lon_grid_to_target()	remove
Grid	lon_remapping	remove
Grid	lon_grid_to_source()	remove
Grid	lon_particle_to_target()	remove
Variable	name	read_only

[VeckoTheGecko]

Once this is merged, I'll do some testing with the team, and then we're good to do a release (from the API POV)