improve docs

[aryarm]

include a listing of the commands and supp fig 1 on the readme

[aryarm]

also...

for simgenotype:

• at the top we might add a sentence as an example. "For example, you could simulate a 50/50 mixture of CEU and YRI for 10 generations. Other more complex models can also be simulated."
• under "--mapdir" "the structure" -> "this structure"
• https://haptools.readthedocs.io/en/latest/formats/sample_info.html: might be helpful to show a couple example rows of the sample info file or directly link to https://github.com/CAST-genomics/haptools/blob/main/example-files/1000genomes_sampleinfo.tsv
• https://haptools.readthedocs.io/en/latest/formats/models.html we might want to say this is based on admix-simu's format. (if breakpoints is also from them, might be good to say so on the breakpoints page as well)
• https://haptools.readthedocs.io/en/latest/formats/maps.html should link to plink map format (https://www.cog-genomics.org/plink/1.9/formats#map) and also mention it is space (or tab?) delimited

for karyogram:

• Usage: https://haptools.readthedocs.io/en/latest/commands/karyogram.html. should mention the breakpoints file can be generated by simgenotype, and link to that

for transform (from @s041629):

• create input and output sections for the transform subcommand and discuss breakpoints files there
• create warning if breakpoints chromosomes don't align with genotypes file chromosomes in transform
• warn better if variants from haplotypes file do not appear in genotypes file

miscellaneous:

• split up the haplotype figure
• when reading breakpoints, make sure that we only split from the last underscore