Remove deprecated codes after dropping GMT 6.4 support

[seisman]

Need to wait for #4127.

Address #4017

[weiji14]

Also need to update these:

1. Remove tolerance from test_subplot_outside_plotting_positioning, xref Update the test_subplot_outside_plotting_positioning test and increase the RMS tolerance #2454. Might need to regenerate the plot

pygmt/pygmt/tests/test_subplot.py

Lines 107 to 110 in 06e75f5

	# Increase tolerance for compatibility with GMT 6.4, see
	# https://github.com/GenericMappingTools/pygmt/pull/2454
	@pytest.mark.mpl_image_compare(tolerance=4.0)
	def test_subplot_outside_plotting_positioning():

2. Remove mention of GMT 6.4 in font parameter of timestamp(), xref Add Figure.timestamp to plot the GMT timestamp logo #2208 (comment) and Allow FONT_LOGO to change font color gmt#7125:

pygmt/pygmt/src/timestamp.py

Lines 52 to 56 in 06e75f5

	font
	Font of the timestamp and the optional label. Since the GMT logo has a fixed
	height, the font sizes are fixed to be 8-point for the timestamp and 7-point for
	the label. The parameter can't change the font color for GMT<=6.4.0, only the
	font style.

3. Update wording on ghostscript transparency note:

pygmt/doc/install.md

Lines 319 to 327 in 06e75f5

	### Not working transparency
	It is known that some combinations of GMT and Ghostscript versions cause issues,
	especially regarding transparency. If the transparency doesn't work in your figures,
	please check your GMT and Ghostscript versions (you can run `pygmt.show_versions()`).
	We recommend:
	- Ghostscript 9.53-9.56 for GMT 6.4.0 (or below)
	- Ghostscript 10.03 or later for GMT 6.5.0

[weiji14]

Ok to merge once tests pass. The ghostscript note can be updated separately, I see you've already opened another branch for that.