README: Update run dev command to use release mode

pixi: Make coverm a project so it can be a source package.

coverm: Add -p minimap2-lr-hq option.

AGENTS.md: Initial effort.

Add option to name cached BAM outputs, rename --bam-file-cache-directory (#266)

fmt: Apply it.

clippy: Apply it.

genome: Do not require checkm-tab-table when min-completeness.

test: filter: Towards large header BAM inputs.

add tolerance to no zeros tests

update galah to include contig clustering

update pixi.lock

restrict minimap to below v2.29

add osx-arm64 to supported platforms

switch to proper pixi platform defined dependencies