parklab/HiScanner ? reverse-engineered prompt

Build me a command line tool for single cell copy number analysis that feels easy to use from the terminal.

I want to be able to initialize a project, fill in a config file and a simple metadata table with BAM files, validate everything, then run the full workflow or just the read depth only version. The full flow should handle SCAN2 results for SNP calling and phasing, then do ADO analysis, normalization, segmentation, and final CNV calling. The simpler mode should skip the SNP and BAF parts and just do the read depth based steps.

Please make it create a clear output folder with separate results for phased variants, ADO, bins, segments, and final calls. It should also have a clean command to remove temporary files. If anything needs current setup details or external docs, look them up online if needed, but keep the user experience simple and straightforward.