refactor: for new haptools release

[aryarm]

This PR refactors a bunch of code ahead of the new v0.3.0 release

• clarifies the documentation around logging
• creates docs for the .linear file format
• slightly changes the behavior of --repeats so that it's only needed if simulating from a mix of haplotype and repeat effects
• bumps our required poetry version
• sorts imports in clump.py and makes them relative
• removes any unnecessary imports
• raises a ValueError instead of using sys.exit in clump.py
• imports from the tr_harmonizer library whenever it is installed rather than use our janky copy of it
• simplifies overrides and revises type hints in GenotypesTR
• fixes a small bug when reading genotypes in GenotypesPLINK whenever the chunksize is not a factor of the overall number of variants
• makes Haplotype.transform and Haplotypes.transform robust to misuse in cases where a Genotypes object where phased info is provided
• allow for logging of exact time using the DEBUG logger
• require effects instead of an entire Haplotypes class in PhenoSimulator.run
• revise bench_genotypes.py to allow for plotting of different chunk sizes and refactor the code to make it easier to work with
• also use new logging library in bench_transform.py and bench_genotypes.py
• bump the current version of the .hap spec to v0.2.0 following the inclusion of repeats in the spec and update all test files to use new version number
• use DATADIR whenever possible in all test files
• describe .ld file format from ld command