Multi-sample phasing in `glimpse2_phase_cram`

[tefirman]

Bug Description

Which module or pipeline has the issue?
ww-glimpse2, ww-imputation

What version are you using?
Latest from main

What went wrong?
The glimpse2_phase_cram task only accepts a single BAM/CRAM file via --bam-file, but GLIMPSE2_phase supports joint multi-sample phasing via --bam-list. The ww-imputation pipeline works around this by scattering over individual samples and phasing each one independently, which doesn't match the recommended usage pattern from the Palantir/Broad GLIMPSE2 workflow.

What did you expect to happen?
glimpse2_phase_cram should accept an array of BAM/CRAM files and use --bam-list to phase all samples jointly in a single call. The ww-imputation pipeline should pass all input CRAMs into each phase call rather than scattering per-sample, producing a single multi-sample output file.

Additional Context

Anything else that might be helpful?

• GLIMPSE2_phase docs describe --bam-file (single) vs --bam-list (multiple) as mutually exclusive input modes
• The fix involves a breaking change to both the ww-glimpse2 task signature (File → Array[File]) and the ww-imputation pipeline inputs (removing ImputationSample struct in favor of flat arrays)
• Both modules are at prototype status so breaking changes are expected