V1 testing

[btmonier]

Summary

This PR re-platforms the assembly alignment steps onto PHGv2's align-assemblies command, adds orchestrator support for the remaining PS4G pipeline steps (ropebwt-mem, build-spline-knots, convert-ropebwt2ps4g), and provides a full "end-to-end" (E2E) suite of integration tests.

Features

• Add commands/align/ shared module (PhgAlignParams, PhgAlignRunner, PhgAlignSharedOptions) and rewrite align-assemblies and align-mutated-assemblies as thin wrappers around PHGv2's align-assemblies (drives AnchorWave + minimap2 internally) while preserving the existing --ref-gff / --ref-fasta / --query-fasta / maf_file_paths.txt contract.
• Add new PHGv2 alignment knobs to both align steps and the YAML config: --in-parallel, --ref-max-align-cov, --query-max-align-cov, --conda-env-prefix, --just-ref-prep.
• Add ropebwt_mem, build_spline_knots, and convert_ropebwt2ps4g sections to orchestrate with output auto-chaining and config dataclasses.
• Add mutated-maf-to-gvcf as a documented orchestrate-only step 11.
• Add a separate Gradle e2eTest task and applyHeavyTestConfig() helper that forks one JVM per heavy test class and restricts class-file scanning so a single fork failure doesn't blow up the whole task.
• Add various Docker improvements for better integration with pixi environments and larger local test memory usage.
• Add IntegrationGuard test helper and ~17 new unit test files covering every pipeline command (AlignAssemblies, AlignMutatedAssemblies, ConvertCoordinates, ConvertRopebwt2Ps4g, ConvertToFasta, CreateChainFiles, DownsampleGvcf, FormatRecombinedFastas, GenerateRecombinedSequences, MafToGvcf, PickCrossovers, RopeBwtChrIndex, RopeBwtMem, PhgAlignRunner) plus a substantially expanded OrchestrateE2ETest.
• Add PHGv2 binary existence check to orchestrate's environment validation so missing PHG triggers an automatic setup-environment retry.

Bug Fixes

• Fix setup-environment failing to find the extracted MLImpute directory after the upstream repo was renamed to grits (archive extracts as grits-main/).
• Fix ropebwt-mem auto-calculating the wrong -l value: the keyfile written by rope-bwt-chr-index/orchestrate has no header row, so the previous lines.size - 1 count was off by one.
• Fix pixi and PHGv2 install permission failures with Docker.

Breaking Changes

• Minor renumbering of pipeline steps (added to docs).
• align-* steps now use PHGv2 instead of AnchorWave directly.

Checklist

• I have updated the version in build.gradle.kts (currently bumped to 0.3.0 in the working tree; commit before opening the PR)
• I have tested these changes locally
• I have added/updated tests for new functionality
• I have updated documentation (if applicable)
• Breaking changes are clearly documented above

[zrm22]

Future idea. Maybe we should change the type to be a data class instead of a Map<String,Any>. It would help not needing to do type casting.

[btmonier]

Totally valid refactoring idea - will consider