Add Flex GEX pipeline support and release helper

[rob-p]

Summary

This branch adds end-to-end support for 10x Flex GEX quantification and the supporting chemistry schema needed to describe Flex protocols in the registry. It also adds a release helper script and cleans up the resulting compile/clippy issues.

Changes compared to dev

• Add a new flex-quant CLI subcommand and wire it into command dispatch.
• Implement the Flex GEX pipeline in src/simpleaf_commands/flex_quant.rs, including:
  • chemistry lookup from the registry
  • automatic probe-set selection by organism
  • probe CSV to FASTA conversion plus probe_t2g.tsv generation
  • cached or on-demand probe index creation with piscem build
  • cell barcode whitelist resolution
  • sample barcode list resolution
  • piscem map-scrna mapping
  • multi-barcode alevin-fry generate-permit-list
  • alevin-fry collate
  • quantification plus pipeline metadata output
• Extend chemistry schema support in src/utils/chem_utils.rs with:
  • Organism enum for organism-specific probe set selection
  • ProtocolType enum to distinguish standard RNA, Flex GEX, and ATAC protocols
  • SampleBcListInfo and ProbeSetInfo structures
  • new sample_bc_list and probe_sets fields on CustomChemistry
  • protocol_type() / is_flex_gex() helpers
  • remote_pl_url serde mapping to the remote_url field used in the registry JSON
• Register Flex chemistries in resources/chemistries.json:
  • 10x-flexv1-gex-3p
  • 10x-flexv2-gex-3p
  • include their geometry strings, protocol metadata, cell barcode whitelist metadata, sample barcode list metadata, and organism-specific probe-set entries for human and mouse
• Update chemistry creation code so newly added custom chemistries initialize the new optional Flex fields to None.
• Relax geometry validation for piscem-only geometry extensions in src/utils/af_utils.rs so geometries containing tags like s[N] or b0[N] skip seq_geom_parser validation and defer validation to piscem.
• Fix Flex-specific pipeline details that differed from the initial implementation:
  • use piscem map-scrna
  • preserve all probes, including excluded probes, in the generated FASTA/t2g mapping so quant has a complete reference-to-gene mapping
  • keep structural constraints enabled only when explicitly requested
• Add bump_and_publish.sh as a release helper script that:
  • validates a requested SemVer version
  • requires the new version to be greater than the current crate version
  • updates both Cargo.toml and the simpleaf entry in Cargo.lock
  • runs preflight/post-bump cargo check and cargo package
  • commits, tags, and pushes the release bump
  • separates dry-run behavior from actual crates.io publishing via --dry-run and --publish
• Update CLI help snapshot(s) to include the new flex-quant command.
• Resolve current compile/clippy issues on this branch:
  • derive Default for ProtocolType
  • replace manual prefix stripping with strip_prefix
  • box the large Chemistry::Custom enum variant

Verification

• cargo build
• cargo clippy --all-targets --all-features -- -D warnings

Notes

• Local untracked data directories/files in the working tree were not included in this PR.