Test MIxS build against linkml main + TSV list normalization demo

[turbomam]

Context

MIxS pins linkml = "^1.9" (resolves to 1.9.4). Recent linkml PRs add configurable list formatting for CSV/TSV (linkml#3134) and boolean handling (linkml#3144). These are on linkml main heading toward v1.10.

MIxS has 463 multivalued slots and 6 boolean slots but zero list/boolean annotations — all guidance is informal ("can be separated by pipes").

What this issue covers

Phase 1: Build compatibility (done)

• Upgrade to linkml main (1.10.0.post78.dev0) + linkml-runtime 1.10.0
• make clean all all-contrib test passes — no regressions

Phase 2: TSV list normalization demo (done)

• Messy TSV example showing 3 real-world list formatting styles (bracketed pipes, bare pipes, spaced pipes)
• Schema-aware normalization script using SchemaView to identify multivalued slots
• Makefile targets: normalize-tsv-demo and normalize-tsv-roundtrip
• Documents that --list-wrapper/--list-delimiter CLI flags exist but json_flattener plumbing isn't connected yet (linkml#3147)

Future phases

• Add schema-level list annotations (list_wrapper, inner_delimiter, list_strip_whitespace)
• Create valid/invalid CSV/TSV example data files
• Tighten slot descriptions to be unambiguous about list formatting

Related issues

• linkml#2581 — Configurable inlined multivalued strings syntax
• linkml#3147 — Validator CSV/TSV loader lacks schema-aware parsing
• linkml#2580 — No truthy values accepted by CSV validation
• Cardinality and syntax of env_broad_scale, env_local_scale, env_medium #1060 — Cardinality and syntax of env triad slots
• specify how the LinkML multivalued metaslot should be used with MIxS terms #952 — Specify how multivalued metaslot should be used with MIxS terms

[turbomam]

Status update: both linkml packages from git main

Pointed both linkml and linkml-runtime at git main in pyproject.toml (previously only linkml was from main; linkml-runtime ^1.10 resolved to 1.10.0 from PyPI, which lacks list_utils.py).

With both packages from the same source:

• linkml-convert --list-wrapper none works for both loading and dumping
• make normalize-tsv-roundtrip passes — bare-pipe TSV → YAML → bare-pipe TSV round-trips correctly
• make normalize-tsv-demo still useful as a pre-normalization step for data that mixes bracket/bare/spaced styles

What still doesn't work:

• linkml-validate with TSV multivalued fields (separate code path, #3147)
• linkml examples (uses the validator loader internally)

Updated the TSV normalization README to reflect current state.

[turbomam]

New blocker: --list-wrapper none crashes on empty multivalued cells (linkml#3250).

When a multivalued column is empty, json_flattener.unflatten_from_csv with bare-pipe markers produces [None], and loader_root.json_clean crashes trying to delete None from the list. This affects any MIxS class with optional multivalued fields (most of them).

Dump side (YAML → bare-pipe TSV) still works. Load side is blocked until #3250 is fixed.

Committed the pyproject.toml + README updates to the branch. Pausing MIxS-side development on this until the linkml fix lands.